Contacts of the helix formed by residues 134 - 148 (chain D) in PDB entry 4K9P
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 GLU 134 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ARG 4.5 6.3 - - - +
105A GLY* 3.2 29.7 + - - +
127D TYR* 2.3 35.3 + - - -
129D PRO* 3.9 7.4 - - + -
130D ALA* 2.7 38.6 + - - +
131D SER* 3.2 18.7 + - - +
132D ALA 3.1 0.8 - - - -
133D ALA* 1.3 78.0 - - - +
135D VAL* 1.3 64.7 + - - +
136D PRO* 3.5 0.9 - - - -
137D HIS* 3.2 15.4 + - + +
138D ALA* 2.9 21.1 + - + +
141D ARG* 4.7 0.9 + - - -
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Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 3.8 16.6 - - + -
8D THR* 4.1 3.6 - - - +
129D PRO* 4.0 14.4 - - + -
131D SER 3.9 4.9 - - - +
132D ALA 3.0 20.0 + - - +
134D GLU* 1.3 76.7 - - - +
136D PRO* 1.3 65.4 - - + +
138D ALA* 3.1 7.9 + - - +
139D MET* 2.9 25.0 + - + +
156D LEU* 4.8 1.1 - - + +
158D VAL* 4.0 18.8 - - + -
162D ASP* 3.5 27.4 - - + +
163D TRP* 4.1 22.9 - - + -
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Residues in contact with PRO 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 3.9 14.6 - - + -
7D THR* 3.9 32.8 - - + -
8D THR* 4.1 16.8 - - - +
11D LEU* 3.3 12.4 - - + +
132D ALA 3.9 1.1 - - - +
133D ALA 3.5 13.5 - - - +
135D VAL* 1.3 93.4 - - + +
137D HIS* 1.3 56.5 + - - +
139D MET* 3.1 7.3 + - + +
140D SER* 2.8 25.6 + - - -
167D ALA* 4.6 5.6 - - + -
171D SER* 4.0 9.4 - - - +
174D LEU* 3.7 13.2 - - + -
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Residues in contact with HIS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 3.4 40.1 - - - -
106A VAL* 3.9 10.1 - - + +
306C ALA 5.4 0.4 - - - -
307C ARG* 2.7 32.8 + - - -
308C ALA 4.6 1.6 - - - -
309C PRO* 4.2 11.3 - - + +
133D ALA 5.0 1.5 + - - +
134D GLU* 3.2 16.9 + - + +
136D PRO* 1.3 79.1 - - - +
138D ALA* 1.3 60.1 + - - +
140D SER* 3.3 2.3 + - - -
141D ARG* 2.9 40.4 + - + +
171D SER* 5.2 1.3 + - - +
174D LEU* 3.6 32.6 - - + +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D TRP* 3.6 4.6 - - - -
127D TYR* 4.1 15.9 - - + -
129D PRO* 4.0 14.1 - - + -
134D GLU* 2.9 14.7 + - - +
135D VAL 3.1 7.6 + - - +
137D HIS* 1.3 76.5 + - - +
139D MET* 1.3 57.7 + - - +
141D ARG* 3.4 14.6 + - - +
142D ALA* 2.9 28.1 + - - +
156D LEU* 3.9 25.1 - - + +
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Residues in contact with MET 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D THR* 4.3 21.1 - - + +
11D LEU* 3.9 13.9 - - + -
12D LEU* 4.1 16.8 - - + -
31D PHE* 5.7 0.2 - - + -
66D PHE* 3.8 27.4 - - + -
93D ILE* 4.3 11.7 - - - -
95D THR* 3.9 14.8 - - + -
135D VAL* 2.9 14.1 + - + +
136D PRO* 3.3 11.9 - - + +
138D ALA* 1.3 73.9 - - - +
140D SER* 1.3 59.9 + - - +
142D ALA* 3.3 2.7 + - - +
143D ILE* 2.9 30.4 + - + +
156D LEU* 3.6 26.9 - - + +
158D VAL* 5.4 0.2 - - + -
163D TRP* 4.7 14.1 - - + -
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Residues in contact with SER 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ALA 4.4 4.0 + - - -
308C ALA 5.1 0.2 + - - -
11D LEU* 3.5 17.2 - - - +
136D PRO 2.8 12.7 + - - -
137D HIS* 3.5 9.6 - - - -
139D MET* 1.3 73.4 - - - +
141D ARG* 1.3 65.6 + - - +
143D ILE* 3.2 7.5 + - - +
144D HIS* 3.1 44.1 + - - -
174D LEU* 3.9 29.4 + - - +
177D ARG* 4.5 6.1 + - - -
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Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE 4.9 0.4 + - - -
105A GLY* 3.1 25.4 + - - -
107A GLU* 2.9 28.3 + - - +
113A VAL* 6.2 0.4 - - - +
303C LEU* 5.3 7.9 + - - +
306C ALA* 3.4 27.9 - - + +
307C ARG* 3.5 24.6 - - - +
125D TRP* 3.3 45.8 - - + +
127D TYR* 4.1 21.2 + - - -
134D GLU* 4.7 0.6 + - - -
137D HIS* 2.9 31.1 + - - +
138D ALA* 3.4 10.1 - - - +
140D SER* 1.3 75.2 + - - +
142D ALA* 1.3 58.8 + - - +
144D HIS 3.3 0.2 + - - -
145D MET* 2.9 35.8 + - + +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 4.2 13.9 - - + -
125D TRP* 3.7 18.8 - - + -
138D ALA 2.9 17.4 + - - +
139D MET* 3.5 9.4 - - - +
140D SER 3.2 0.2 - - - -
141D ARG* 1.3 75.0 - - - +
143D ILE* 1.3 63.5 + - - +
145D MET* 3.9 0.8 - - - +
146D ALA* 3.1 20.3 + - - +
154D VAL* 3.4 25.8 - - + +
155D TYR 5.7 0.2 - - - +
156D LEU* 4.7 13.2 - - + -
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.1 16.4 - - + +
12D LEU* 4.0 23.8 - - + -
15D GLN* 4.0 42.0 - - + +
17D ILE* 4.1 9.6 - - + -
64D PRO* 5.4 2.7 - - + -
93D ILE* 3.8 26.7 - - + +
139D MET* 2.9 22.5 + - + +
140D SER* 3.5 7.9 - - - +
142D ALA* 1.3 76.8 - - - +
144D HIS* 1.3 68.7 + - + +
146D ALA* 3.5 2.1 + - - +
147D SER* 2.8 34.2 + - - +
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Residues in contact with HIS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ALA* 4.1 18.4 - - + -
11D LEU* 6.2 0.2 - - - +
15D GLN* 3.6 29.1 + - - +
140D SER* 3.1 38.8 + - - +
143D ILE* 1.3 77.9 - - + +
145D MET* 1.3 62.0 + - - +
147D SER* 4.4 5.7 - - - +
148D MET* 2.9 40.6 + - + +
174D LEU 5.2 0.8 + - - -
177D ARG* 3.6 43.0 - - - +
179D VAL* 3.3 31.8 - - + +
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C PRO* 3.9 14.8 - - + +
303C LEU* 4.0 27.1 - - + -
306C ALA* 3.6 14.1 - - + -
124D LYS* 2.6 69.7 + - + +
125D TRP* 4.2 20.4 - - + -
141D ARG* 2.9 22.5 + - + +
142D ALA* 3.9 1.1 - - - +
144D HIS* 1.3 77.8 - - - +
146D ALA* 1.3 59.4 + - - +
148D MET* 3.5 21.0 + - + +
154D VAL* 3.9 16.2 - - + -
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PRO* 5.3 0.2 - - + -
91D PRO* 3.6 8.5 - - + +
92D LEU 4.2 9.4 - - - +
93D ILE* 4.1 13.5 - - + -
142D ALA 3.1 17.6 + - - +
143D ILE 3.9 3.6 - - - +
145D MET* 1.3 78.6 - - - +
147D SER* 1.3 57.5 + - - +
151D GLN* 3.4 11.8 - - - +
152D GLY 3.3 40.8 + - - +
154D VAL* 3.7 14.8 - - + +
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PRO* 3.6 28.3 - - - +
91D PRO* 4.7 1.1 - - - -
143D ILE* 2.8 22.6 + - - +
144D HIS* 3.3 6.5 + - - -
146D ALA* 1.3 75.8 - - - +
148D MET* 1.3 64.7 + - - +
149D ALA 3.8 0.5 + - - -
151D GLN* 2.9 29.5 + - - +
181D SER* 4.8 1.7 + - - -
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Residues in contact with MET 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C PRO* 3.2 37.5 - - + +
305C ALA* 4.0 2.5 - - - -
306C ALA* 3.5 11.7 - - + +
315C VAL* 3.8 18.4 - - + -
124D LYS* 3.3 10.0 + - - +
144D HIS 2.9 26.4 + - - +
145D MET* 3.5 24.7 + - - +
146D ALA 3.6 0.2 - - - -
147D SER* 1.3 78.5 - - - +
149D ALA* 1.3 64.7 + - - +
150D PRO 3.1 18.7 - - - +
151D GLN* 3.2 4.5 + - - -
179D VAL* 3.4 35.9 - - + +
181D SER* 3.9 11.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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