Contacts of the helix formed by residues 125 - 141 (chain B) in PDB entry 3LKB
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 SER 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 3.1 16.8 - - - -
108B ILE* 3.8 28.8 - - - +
121B LEU* 4.5 4.2 - - - +
123B THR 4.5 0.4 - - - -
124B THR* 1.3 76.1 - - - +
126B TYR* 1.3 65.6 + - - +
127B SER 3.8 2.0 + - - -
128B GLU* 3.3 22.9 + - - +
129B GLN* 3.0 27.6 + - - +
351B THR* 5.5 1.0 - - - +
378B PHE* 3.8 15.6 - - - -
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.6 23.1 - - + -
106B MET* 3.0 44.6 + - + +
107B HIS* 3.7 9.9 - - + -
125B SER* 1.3 71.9 - - - +
127B SER* 1.3 61.5 + - - +
129B GLN* 3.2 17.8 + - - +
130B VAL* 2.8 34.8 + - - +
155B PHE* 3.8 3.1 - + - -
158B ALA* 3.9 10.5 - - + -
159B PRO* 3.8 15.3 - - + -
205B GLN* 3.2 35.4 - - - +
230B ALA* 4.9 0.8 - - + +
231B HIS* 5.3 0.7 - - + -
232B TYR* 3.3 30.6 - + - -
393B VAL* 2.4 29.9 - - + +
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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
----------------------------------------------------------
107B HIS* 5.0 1.6 - - - -
108B ILE* 3.9 12.7 - - - +
125B SER* 3.2 4.4 - - - -
126B TYR* 1.3 80.2 - - - +
128B GLU* 1.3 56.2 + - - +
130B VAL* 3.4 0.7 + - - +
131B VAL* 2.8 37.3 + - - +
158B ALA 4.1 3.8 + - - -
159B PRO* 3.6 25.6 - - - +
162B ASP* 2.8 34.6 + - - -
163B ALA 5.7 0.4 + - - +
378B PHE* 3.6 13.9 - - - -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B THR* 3.8 17.2 + - + -
125B SER* 3.3 19.7 + - - +
126B TYR 3.3 0.6 - - - -
127B SER* 1.3 79.3 - - - +
129B GLN* 1.3 59.1 + - - +
131B VAL* 3.7 0.9 - - - +
132B ALA* 2.8 29.1 + - - +
351B THR* 6.1 0.7 - - - +
354B GLU* 4.2 5.9 - - - +
356B LEU* 4.1 14.4 - - + -
374B THR* 3.5 7.1 - - - -
375B SER* 2.8 34.1 + - - -
378B PHE* 3.7 33.9 - - + -
379B ARG* 3.0 21.4 + - - -
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 3.7 15.4 - - - -
123B THR* 4.4 2.4 + - - -
124B THR* 3.2 40.4 + - + +
125B SER 3.0 12.9 + - - +
126B TYR* 3.6 13.8 - - - +
128B GLU* 1.3 76.1 - - - +
130B VAL* 1.3 59.2 + - - +
132B ALA* 3.3 2.6 + - - +
133B LEU* 3.0 33.7 + - - +
230B ALA* 3.5 12.6 - - + +
231B HIS* 2.9 33.3 + - - +
252B ALA* 3.9 19.6 - - + +
253B THR* 5.0 4.0 - - - +
254B SER* 5.2 1.0 + - - +
356B LEU* 3.9 12.6 - - + -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR 2.8 22.3 + - - +
127B SER 4.1 2.5 - - - +
129B GLN* 1.3 74.6 - - - +
131B VAL* 1.3 55.9 + - - +
133B LEU* 3.3 7.3 + - + +
134B LEU* 3.0 31.3 + - + +
148B LEU* 5.2 4.3 - - + -
159B PRO* 4.0 22.9 - - + -
163B ALA* 3.7 30.7 - - + +
203B VAL* 4.2 24.9 - - + -
205B GLN* 5.0 4.9 - - + -
230B ALA* 4.2 17.3 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER 2.8 32.3 + - - +
128B GLU 3.9 2.9 - - - +
130B VAL* 1.3 70.6 - - - +
132B ALA* 1.3 63.7 + - - +
134B LEU* 3.4 8.6 + - - +
135B GLU* 3.0 25.2 + - - +
162B ASP* 4.2 20.0 - - + +
163B ALA 4.7 1.6 - - - +
166B ALA* 4.0 17.7 - - + -
375B SER* 3.7 20.2 - - - +
377B LEU* 4.1 17.3 - - + -
378B PHE* 3.8 23.1 - - + +
381B VAL* 4.7 2.0 - - + -
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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
----------------------------------------------------------
128B GLU 2.8 19.0 + - - +
129B GLN 3.6 4.7 - - - +
131B VAL* 1.3 75.8 - - - +
133B LEU* 1.3 63.6 + - - +
135B GLU* 3.2 14.7 + - - +
136B TYR* 3.0 19.9 + - - +
252B ALA* 5.2 1.6 - - + -
356B LEU* 4.2 12.6 - - + -
358B ILE* 4.0 9.2 - - + +
373B PHE* 4.1 30.6 - - + -
375B SER* 4.9 4.5 - - - -
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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 GLN 3.0 20.1 + - - +
130B VAL* 3.5 6.1 - - - +
131B VAL 3.2 0.2 - - - -
132B ALA* 1.3 75.4 - - - +
134B LEU* 1.3 59.8 + - - +
136B TYR* 3.1 8.1 + - + +
137B ILE* 2.9 31.6 + - - +
203B VAL* 4.1 18.8 - - + -
228B LEU* 4.1 21.8 - - + +
229B GLY* 3.3 41.7 - - - +
230B ALA* 3.8 3.8 - - - +
250B LEU 4.1 14.8 - - - +
252B ALA* 3.9 19.3 - - + +
358B ILE* 4.1 20.2 - - + -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.0 22.3 + - + +
131B VAL* 3.4 5.1 + - - +
133B LEU* 1.3 76.8 - - - +
135B GLU* 1.3 57.2 + - - +
137B ILE* 3.3 8.8 + - + +
138B ALA 3.0 22.3 + - - -
146B VAL* 4.0 26.7 - - + -
148B LEU* 4.9 5.6 - - + -
163B ALA* 3.5 40.2 - - + +
166B ALA* 4.0 12.1 - - + -
167B ALA* 4.1 9.6 - - + +
170B LEU* 3.5 15.0 - - + +
172B LEU* 3.5 20.0 - - + +
174B ILE* 5.0 2.9 - - + -
203B VAL* 4.1 15.9 - - + -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL 3.0 16.1 + - - +
132B ALA* 3.3 11.8 - - - +
134B LEU* 1.3 75.7 - - - +
136B TYR* 1.3 65.2 + - - +
138B ALA* 3.2 10.9 + - - +
139B ARG* 3.3 18.0 + - - +
170B LEU* 4.1 13.9 - - + +
373B PHE* 5.5 2.7 - - + -
375B SER* 2.7 31.8 + - - -
376B ALA 5.3 0.3 + - - -
377B LEU* 3.6 37.8 + - + +
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA 3.0 12.6 + - - +
133B LEU* 3.3 10.5 - - + +
135B GLU* 1.3 77.6 - - - +
137B ILE* 1.3 64.6 + - + +
139B ARG* 3.6 41.1 - - - +
140B GLU* 3.4 44.5 + - + +
201B TYR* 6.1 1.3 - + - -
226B ARG* 4.0 11.1 + - - -
228B LEU* 4.6 6.5 - - + -
250B LEU* 3.4 34.4 - - + +
358B ILE* 4.0 28.3 - - + -
360B GLU* 5.1 2.3 + - - -
369B VAL* 4.2 24.2 - - + +
370B THR* 5.4 1.8 - - + -
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Residues in contact with ILE 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 2.9 19.0 + - - +
134B LEU* 3.6 17.7 - - + +
135B GLU 3.2 0.2 - - - -
136B TYR* 1.3 78.1 - - + +
138B ALA* 1.3 56.9 + - - +
140B GLU* 3.3 5.8 + - - +
141B LYS* 2.9 26.5 + - - +
144B ALA* 3.9 14.4 - - + -
146B VAL* 4.2 10.1 - - + -
172B LEU* 4.2 5.2 - - + -
201B TYR* 3.7 50.0 - - + -
203B VAL* 3.7 29.6 - - + -
228B LEU* 3.8 17.7 - - + -
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Residues in contact with ALA 138 (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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134B LEU 3.0 15.3 + - - +
135B GLU 3.2 3.3 + - - +
137B ILE* 1.3 76.7 - - - +
139B ARG* 1.3 59.6 + - - +
140B GLU 3.6 0.2 + - - -
141B LYS 3.7 7.3 + - - -
142B LYS* 3.0 31.4 + - + +
170B LEU* 3.9 33.4 - - + +
172B LEU* 3.8 21.3 - - + +
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Residues in contact with ARG 139 (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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135B GLU 3.3 14.4 + - - +
136B TYR* 3.6 47.6 + - - +
138B ALA* 1.3 76.8 - - - +
140B GLU* 1.3 67.6 + - - +
142B LYS* 3.8 13.8 + - - +
369B VAL* 5.8 2.4 + - - +
370B THR* 5.4 7.3 - - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 3.4 41.4 + - + +
137B ILE* 3.3 6.1 + - - +
138B ALA 3.3 0.2 - - - -
139B ARG* 1.3 85.1 + - - +
141B LYS* 1.3 57.6 + - - +
142B LYS 4.3 0.4 - - - -
201B TYR* 3.3 30.8 + - - +
226B ARG* 4.3 17.2 + - - +
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Residues in contact with LYS 141 (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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137B ILE 2.9 13.1 + - - +
138B ALA 3.9 1.6 - - - -
139B ARG 3.6 1.4 - - - -
140B GLU* 1.3 80.1 - - - +
142B LYS* 1.3 76.0 + - - +
143B GLY 3.4 0.5 + - - -
144B ALA* 3.1 32.5 + - + +
172B LEU* 4.0 4.2 - - - +
200B GLU* 3.6 29.3 + - + +
201B TYR* 3.3 25.1 - - + +
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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