Contacts of the helix formed by residues 124 - 144 (chain B) in PDB entry 2WLV
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 PRO 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B MET* 4.4 9.6 - - + +
122B PRO 4.1 4.9 - - - +
123B VAL* 1.4 83.0 - - + +
125B VAL* 1.4 64.3 + - - +
126B GLY 3.2 2.7 - - - -
127B ASN* 3.0 24.5 + - + +
128B ILE* 3.0 32.9 + - + +
131B ARG* 6.1 0.9 - - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 3.8 23.7 - - + +
97B PRO* 4.0 14.6 - - + -
102B ILE* 3.7 28.5 - - + +
112B GLN* 3.9 19.7 - - + +
115B TRP* 4.1 10.3 - - + -
116B MET* 3.8 17.1 - - + +
123B VAL* 2.8 34.6 + - + +
124B PRO* 1.4 71.9 - - - +
126B GLY* 1.3 64.4 + - - +
128B ILE* 4.3 6.7 - - - -
129B TYR* 3.0 25.5 + - - +
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Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B CYS 3.4 23.6 - - - -
47B THR* 4.4 0.9 - - - -
48B PRO* 3.8 15.0 - - - +
51B ILE* 3.6 4.9 - - - +
116B MET* 4.1 7.3 - - - +
124B PRO 3.2 0.8 - - - -
125B VAL* 1.3 83.9 - - - +
127B ASN* 1.3 60.0 + - - +
129B TYR* 3.4 1.0 + - - +
130B ARG* 2.9 32.6 + - - +
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY* 5.0 7.1 + - - -
46B CYS 5.1 2.4 - - - +
116B MET* 5.9 0.4 - - - +
124B PRO* 3.0 24.0 + - + +
126B GLY* 1.3 73.9 - - - +
128B ILE* 1.3 65.3 + - - +
130B ARG* 3.3 35.2 + - - +
131B ARG* 3.2 30.6 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 3.8 32.8 - - + -
102B ILE* 3.8 10.3 - - + -
123B VAL* 3.9 17.7 - - + -
124B PRO* 3.0 30.2 + - + +
125B VAL* 3.9 6.5 - - - +
127B ASN* 1.3 76.8 - - - +
129B TYR* 1.3 62.9 + - - +
131B ARG* 3.1 42.2 + - - +
132B TRP* 3.2 49.5 + - + +
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 3.8 16.2 - - + -
51B ILE* 3.5 26.0 - - + -
52B ASN* 2.7 25.8 + - - -
55B LEU* 3.5 12.1 - - - +
69B ARG* 4.7 3.1 + - - -
72B ILE* 3.7 17.5 - - + +
102B ILE* 3.4 20.2 - - + +
103B ALA* 3.4 35.4 + - + +
125B VAL 3.0 18.0 + - - +
126B GLY 3.7 3.4 - - - +
128B ILE* 1.3 74.9 - - - +
130B ARG* 1.3 67.0 + - - +
132B TRP* 3.0 21.2 + + + -
133B ILE* 2.9 41.8 + - + +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.8 15.2 - - + -
40B GLN* 2.8 60.3 + - - +
43B SER* 2.8 39.4 + - - +
44B GLU* 3.5 27.8 + - - +
46B CYS 5.1 2.5 - - - +
51B ILE* 3.5 17.7 - - + +
126B GLY 2.9 22.0 + - - +
127B ASN* 3.3 36.7 + - - +
128B ILE 3.3 0.2 - - - -
129B TYR* 1.3 76.6 - - - +
131B ARG* 1.3 55.9 + - - +
133B ILE* 3.3 1.4 + - - -
134B GLN* 2.9 29.0 + - - +
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TRP* 5.4 4.6 - - - -
124B PRO* 6.1 0.8 - - - +
127B ASN* 3.2 14.6 + - - +
128B ILE* 3.1 48.1 + - - +
130B ARG* 1.3 79.5 - - - +
132B TRP* 1.3 72.0 + - + +
134B GLN* 3.2 15.4 + - - +
135B ILE* 3.0 30.3 + - + +
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Residues in contact with TRP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 5.6 0.3 - - - +
71B ILE* 3.6 7.8 - - - +
72B ILE* 4.1 19.8 - - + +
75B GLU* 3.4 51.7 + - + +
76B ALA* 3.7 25.6 - - + -
79B TRP* 4.1 11.9 - + + -
99B GLY* 3.7 23.6 - - - -
102B ILE* 3.5 21.5 - - + -
103B ALA* 4.3 6.7 - - + -
128B ILE* 3.3 38.1 - - + +
129B TYR* 3.0 25.1 + + + +
131B ARG* 1.3 88.0 - - + +
133B ILE* 1.3 62.1 + - - +
135B ILE* 3.3 12.8 + - + +
136B GLY* 3.1 16.5 + - - -
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Residues in contact with ILE 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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22B TRP* 6.2 0.4 - - + -
39B PHE* 3.5 33.0 - - + -
51B ILE* 3.8 20.4 - - + -
55B LEU* 3.9 25.1 - - + -
68B ILE* 3.9 10.2 - - + +
72B ILE* 3.6 33.7 - - + -
129B TYR* 2.9 30.8 + - + +
130B ARG 3.8 1.3 - - - +
132B TRP* 1.3 72.7 - - - +
134B GLN* 1.3 61.1 + - - +
136B GLY* 3.1 3.5 + - - +
137B LEU* 2.8 41.6 + - + +
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 3.9 23.3 + - + +
39B PHE* 4.5 4.9 - - + -
40B GLN* 3.6 33.7 + - - +
130B ARG 2.9 13.2 + - - +
131B ARG* 3.2 16.5 + - - +
133B ILE* 1.3 76.9 - - - +
135B ILE* 1.3 58.4 + - + +
137B LEU* 3.8 9.4 - - - +
138B GLN* 2.8 57.9 + - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.6 25.6 - - + -
75B GLU* 4.1 30.5 - - + +
131B ARG* 3.0 19.4 + - + +
132B TRP* 3.5 9.4 - - + +
134B GLN* 1.3 76.4 - - + +
136B GLY* 1.3 62.0 + - - +
138B GLN* 3.4 14.6 + - - +
139B LYS* 3.1 21.6 + - + +
142B ARG* 5.1 2.2 + - - +
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.8 2.0 - - - +
68B ILE* 4.0 17.9 - - - -
71B ILE* 3.9 22.1 - - - +
132B TRP 3.1 7.1 + - - -
133B ILE* 3.1 7.4 + - - -
135B ILE* 1.3 79.0 - - - +
137B LEU* 1.3 56.4 + - - +
139B LYS* 3.2 5.1 + - - +
140B CYS* 2.9 30.5 + - - -
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Residues in contact with LEU 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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22B TRP* 4.1 16.2 - - + -
31B PHE* 4.1 21.3 - - + -
35B VAL* 4.1 16.2 - - + +
36B VAL* 4.0 14.8 - - + -
39B PHE* 3.4 42.2 - - + -
55B LEU* 6.3 0.4 - - + -
58B VAL* 5.6 0.7 - - + -
68B ILE* 3.9 20.0 - - + -
133B ILE* 2.8 31.9 + - + +
134B GLN* 3.9 4.9 - - - +
136B GLY* 1.3 69.8 - - - +
138B GLN* 1.3 66.5 + - - +
140B CYS* 3.1 5.5 + - - +
141B VAL* 2.9 26.7 + - - +
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Residues in contact with GLN 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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36B VAL* 3.9 25.4 - - + +
134B GLN* 2.8 42.4 + - - +
135B ILE* 3.7 16.9 - - - +
137B LEU* 1.3 78.0 - - - +
139B LYS* 1.3 61.7 + - - +
141B VAL* 3.3 6.0 + - - +
142B ARG* 3.1 41.9 + - - +
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Residues in contact with LYS 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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67B ILE* 3.6 20.7 + - + +
70B GLU* 4.2 19.2 + - - -
71B ILE* 4.0 28.2 - - + +
74B GLU* 5.4 1.8 + - - -
135B ILE* 3.1 13.9 + - + +
136B GLY* 3.5 9.0 - - - +
137B LEU 3.2 0.2 - - - -
138B GLN* 1.3 74.7 - - - +
140B CYS* 1.3 65.6 + - - +
142B ARG* 3.2 27.9 + - - +
143B MET* 2.9 52.6 + - + +
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Residues in contact with CYS 140 (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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31B PHE* 4.0 22.2 - - + -
64B ALA* 3.6 42.2 - - - -
67B ILE* 3.9 16.5 - - - +
68B ILE* 3.8 13.2 - - - -
136B GLY 2.9 20.1 + - - -
137B LEU* 3.5 8.1 - - - +
139B LYS* 1.3 76.3 - - - +
141B VAL* 1.3 64.5 + - - +
144B TYR* 2.9 34.0 + - + +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.4 21.9 - - - +
32B GLY* 3.5 14.4 - - - +
33B ALA* 3.9 28.5 - - + +
35B VAL* 3.8 12.6 - - + -
36B VAL* 4.1 9.2 - - + -
137B LEU 2.9 18.5 + - - +
138B GLN* 3.6 9.2 - - - +
139B LYS 3.2 0.2 - - - -
140B CYS* 1.3 79.6 - - - +
142B ARG* 1.3 62.2 + - + +
143B MET 3.5 0.2 + - - -
144B TYR* 3.9 9.2 + - - +
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Residues in contact with ARG 142 (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 ILE* 5.1 1.6 + - - +
138B GLN* 3.1 35.7 + - - +
139B LYS* 3.6 38.2 - - - +
141B VAL* 1.3 80.4 - - + +
143B MET* 1.4 60.3 + - + +
144B TYR 5.0 1.3 - - - +
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Residues in contact with MET 143 (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 ILE* 3.7 33.9 - - + -
139B LYS* 2.9 48.1 + - + +
140B CYS 4.2 0.2 - - - +
142B ARG* 1.4 79.7 - - + +
144B TYR* 1.4 67.0 + - - +
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Residues in contact with TYR 144 (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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30B LYS* 3.8 25.1 - - + +
31B PHE* 3.6 29.2 - + + +
61B HIS* 4.0 14.8 + - - +
63B ALA* 3.6 17.4 - - + +
64B ALA* 3.1 43.4 + - + +
67B ILE* 4.7 6.1 - - + -
140B CYS* 2.9 30.7 + - + +
141B VAL 3.9 7.7 + - - +
142B ARG 3.8 2.4 - - - +
143B MET* 1.4 80.0 - - - +
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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