Contacts of the helix formed by residues 118 - 139 (chain B) in PDB entry 4KIK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 6.3 0.6 - - - +
113B ASN* 4.8 5.3 + - - +
117B LEU* 1.4 78.1 - - - +
119B GLU* 1.3 65.1 + - - +
120B GLY 3.3 1.3 - - - +
121B ALA* 3.2 9.0 + - + +
122B ILE* 3.1 19.6 + - - +
264B ASN* 3.7 16.6 - - + +
378B GLU 4.4 15.9 - - - +
379B GLY* 4.6 17.5 + - - -
381B THR* 4.9 19.8 - - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU 4.0 0.2 + - - -
118B ARG* 1.3 71.7 - - - +
120B GLY* 1.3 62.1 + - - +
122B ILE* 3.3 11.8 + - - +
123B LEU* 3.1 32.1 + - + +
264B ASN 3.6 18.8 + - - +
265B LEU* 3.6 7.9 - - + -
266B ASN* 2.9 52.8 + - - +
269B LEU* 3.5 21.6 - - + +
311B LEU* 5.4 0.2 - - - +
313B HIS* 4.9 4.9 + - - -
380B HIS* 4.8 10.9 + - + +
381B THR* 5.3 8.0 - - + +
382B LEU* 4.9 14.9 + - - +
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 3.3 1.2 - - - +
119B GLU* 1.3 75.9 - - - +
121B ALA* 1.3 56.6 + - - +
123B LEU* 3.3 11.0 + - - +
124B THR* 3.1 32.6 + - - +
377B ASN 3.6 16.8 - - - -
378B GLU* 3.6 11.9 + - - -
380B HIS* 3.4 22.3 + - - -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.0 26.0 - - + +
118B ARG* 3.2 15.6 + - + +
120B GLY* 1.3 73.9 - - - +
122B ILE* 1.4 56.7 + - - +
124B THR* 3.4 8.9 + - - -
125B LEU* 3.2 27.2 + - - +
162B HIS* 4.1 5.3 + - - +
378B GLU* 3.6 23.5 + - + +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.3 33.0 - - + +
118B ARG 3.1 10.6 + - - +
119B GLU* 3.6 6.5 - - - +
120B GLY 3.3 0.4 - - - -
121B ALA* 1.4 73.3 - - - +
123B LEU* 1.3 61.5 + - + +
125B LEU* 3.3 8.7 + - + +
126B LEU* 2.9 55.2 + - + +
212B ALA 5.6 0.4 - - - +
215B CYS* 3.9 22.2 - - + +
216B ILE* 3.9 29.8 - - + +
264B ASN 5.6 0.7 - - - +
265B LEU* 3.9 30.3 - - + +
273B LEU* 4.4 2.7 - - + -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 3.1 26.9 + - + +
120B GLY* 3.8 9.0 - - - +
122B ILE* 1.3 77.5 - - + +
124B THR* 1.4 57.0 + - + +
126B LEU* 3.9 8.5 - - + +
127B SER* 3.1 30.1 + - - -
269B LEU* 3.9 41.1 - - + -
273B LEU* 5.5 0.7 - - + -
306B ILE* 5.7 0.9 - - + +
307B LEU* 3.4 32.7 - - + +
376B LEU* 6.6 0.2 - - + -
380B HIS* 5.4 10.1 - - + -
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY 3.1 14.6 + - - +
121B ALA* 3.4 10.4 + - - -
123B LEU* 1.4 74.0 - - + +
125B LEU* 1.4 63.0 + - - +
127B SER* 4.5 3.6 - - - -
128B ASP* 3.0 33.0 + - - +
159B ARG* 3.7 32.5 - - - +
160B LEU 4.7 1.9 + - - -
162B HIS* 3.2 18.0 - - - -
376B LEU 4.5 4.7 - - - +
377B ASN* 4.1 22.4 - - - +
378B GLU* 4.3 5.7 + - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.7 27.4 - - + -
117B LEU* 5.4 1.8 - - + -
121B ALA 3.2 16.8 + - - +
122B ILE* 3.5 8.7 - - + +
124B THR* 1.4 80.4 + - - +
126B LEU* 1.3 68.3 + - + +
128B ASP* 3.8 0.5 - - - +
129B ILE* 2.9 51.5 + - + +
151B ILE* 4.5 3.1 - - + -
162B HIS* 3.5 30.3 - - + +
208B PHE* 5.4 1.1 - - + -
211B LEU* 4.2 11.9 - - + -
212B ALA* 4.6 8.1 - - - +
215B CYS* 3.8 31.4 - - + -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 2.9 39.8 + - + +
123B LEU* 3.9 10.1 - - + +
125B LEU* 1.3 78.7 - - + +
127B SER* 1.3 56.6 + - - +
130B ALA* 2.9 34.3 + - - +
208B PHE* 3.6 12.4 - - + -
212B ALA* 3.9 28.7 - - + -
216B ILE* 5.3 2.7 - - + -
273B LEU* 3.8 28.0 - - + -
276B TRP* 4.0 22.7 - - + -
303B LEU* 4.2 17.5 - - + -
307B LEU* 4.6 4.0 - - + -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU 3.1 17.4 + - - -
124B THR* 4.0 5.4 - - - -
126B LEU* 1.3 78.3 - - - +
128B ASP* 1.4 64.7 + - - +
130B ALA* 4.1 3.0 - - - +
131B SER* 3.2 25.3 + - - -
134B ARG* 5.6 0.5 + - - -
307B LEU* 3.7 24.5 - - - +
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 3.3 41.4 + - - +
124B THR* 3.0 16.7 + - - +
125B LEU 3.8 0.2 - - - +
127B SER* 1.4 83.1 + - - +
129B ILE* 1.3 59.9 + - - +
131B SER* 4.7 0.2 - - - -
132B ALA* 3.3 19.9 + - - +
159B ARG* 2.8 42.7 + - - -
162B HIS* 2.8 39.4 + - + +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 2.9 30.9 + - + +
128B ASP* 1.3 75.3 - - - +
130B ALA* 1.3 65.6 + - - +
132B ALA* 3.4 2.6 + - + +
133B LEU* 3.0 23.8 + - + +
146B LEU* 4.5 9.4 - - + -
151B ILE* 3.8 39.5 - - + -
162B HIS* 3.9 26.2 - - + -
163B LYS* 4.5 0.4 - - - +
164B ILE* 3.9 26.2 - - + -
208B PHE* 3.5 33.2 - - + -
211B LEU* 5.3 0.2 - - + -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU 2.9 20.7 + - - +
127B SER* 4.1 4.0 - - - +
129B ILE* 1.3 73.9 - - - +
131B SER* 1.4 57.0 + - - +
133B LEU* 3.5 2.1 + - - +
134B ARG* 2.9 43.5 + - - +
208B PHE* 3.6 14.0 - - + -
300B PHE* 3.8 17.1 - - + -
303B LEU* 3.6 22.7 - - + -
307B LEU* 5.7 0.2 - - + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B HIS* 3.3 30.1 + - - -
72B ASN* 4.0 6.0 + - - -
127B SER 3.2 18.2 + - - -
128B ASP 3.9 4.9 - - - -
130B ALA* 1.4 78.9 - - - +
132B ALA* 1.3 55.8 + - - +
134B ARG* 3.6 24.4 + - - +
135B TYR 3.2 19.6 + - - -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B HIS* 4.0 8.0 - - - -
72B ASN* 3.3 27.6 - - + +
73B VAL* 3.8 9.7 - - + +
128B ASP 3.3 13.5 + - - +
129B ILE* 3.7 2.2 - - + +
130B ALA 3.3 0.2 - - - -
131B SER* 1.3 76.8 - - - +
133B LEU* 1.4 59.2 + - - +
135B TYR* 3.2 5.0 + - - +
136B LEU* 3.0 31.4 + - - +
164B ILE* 3.5 23.8 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ILE* 3.0 15.8 + - + +
130B ALA 3.8 3.6 - - - +
132B ALA* 1.4 71.8 - - - +
134B ARG* 1.3 55.4 + - - +
136B LEU* 3.3 12.1 + - + -
137B HIS* 2.8 65.2 + - + +
143B HIS* 4.7 2.7 - - + -
146B LEU* 3.7 34.5 - - + -
164B ILE* 4.1 13.0 - - + -
204B ASP* 3.8 24.7 - - + +
205B TYR* 5.3 0.7 - - + -
208B PHE* 3.8 24.9 - - + -
300B PHE* 3.8 13.9 - - + -
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER 5.6 0.4 + - - -
130B ALA* 2.9 31.6 + - - +
131B SER* 3.6 27.6 + - - +
133B LEU* 1.3 73.3 - - - +
135B TYR* 1.4 58.9 + - - +
137B HIS* 4.2 1.9 - - - +
138B GLU* 2.9 61.9 + - + +
300B PHE* 3.3 53.7 + - + +
301B LYS* 6.1 1.6 - - - +
303B LEU* 5.8 0.2 - - - +
304B ASP* 3.2 33.7 + - - -
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Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ARG 4.3 1.2 + - - -
68B LEU* 3.5 33.1 - - + +
69B THR* 2.9 52.7 + - + +
70B HIS* 3.5 40.2 - + + -
73B VAL* 4.4 9.4 - - + -
131B SER 3.2 4.8 + - - +
132B ALA 3.2 7.6 + - - +
134B ARG* 1.4 75.8 - - - +
136B LEU* 1.3 67.6 + - + +
138B GLU* 3.5 7.7 + - - -
139B ASN* 2.8 57.9 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.6 38.4 - - + -
73B VAL* 4.8 7.6 - - + -
132B ALA 3.0 18.3 + - - +
133B LEU* 3.3 18.1 + - + +
135B TYR* 1.3 79.3 - - + +
137B HIS* 1.3 63.3 + - + +
139B ASN* 3.0 12.0 + - - -
140B ARG 3.1 0.3 + - - -
141B ILE* 2.9 49.0 + - + +
143B HIS* 4.3 24.5 - - + +
164B ILE* 4.7 10.8 - - + -
167B LEU* 4.3 17.3 - - + -
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 2.8 36.4 + - + +
134B ARG* 4.2 3.8 - - - +
136B LEU* 1.3 76.8 - - + +
138B GLU* 1.4 56.4 + - + +
140B ARG* 3.1 22.0 + - - +
141B ILE 3.3 19.5 - - - +
173B LEU* 5.5 0.3 - - - +
201B VAL* 3.8 30.8 - - + +
204B ASP* 2.8 41.6 + - + +
205B TYR* 3.7 30.4 + + - -
300B PHE* 4.1 9.2 - + + -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 2.9 49.6 + - + +
135B TYR* 4.0 7.6 - - - +
137B HIS* 1.4 70.4 - - - +
139B ASN* 1.4 61.3 + - - +
140B ARG* 3.1 14.3 + - - +
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 2.8 33.9 + - - +
68B LEU* 4.9 3.4 - - + -
135B TYR* 2.8 61.3 + - - +
136B LEU* 3.0 7.1 + - - +
138B GLU* 1.4 79.3 + - - +
140B ARG* 1.3 64.5 + - - +
141B ILE* 3.3 13.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il