Contacts of the helix formed by residues 136 - 153 (chain B) in PDB entry 2HYM
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 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 5.5 2.7 - - - -
133B LYS* 2.6 25.7 + - - +
134B LYS* 4.3 3.9 + - - +
135B TYR* 1.3 77.2 - - - +
137B PRO* 1.3 77.6 - - - +
138B CYS* 3.4 1.6 - - - -
139B ALA* 3.0 17.7 + - - +
140B TRP* 3.0 23.5 + - - -
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Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 6.4 1.3 - - + -
24B ILE* 3.6 25.0 - - + +
76B TRP* 5.5 0.2 - - - -
135B TYR 4.0 2.0 - - - +
136B SER* 1.3 87.5 - - - +
138B CYS* 1.3 66.3 + - - +
140B TRP* 3.1 21.4 + - + +
141B GLU* 3.2 8.3 + - - +
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Residues in contact with CYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.7 8.5 - - - -
26B LEU* 4.1 1.4 - - - +
29B CYS* 2.0 55.4 - - + -
31B LYS* 6.2 1.6 - - + -
32B ASP* 3.6 19.3 - - + +
136B SER* 3.4 1.6 - - - -
137B PRO* 1.3 84.4 - - - +
139B ALA* 1.3 62.0 + - - +
141B GLU* 3.1 13.2 + - - +
142B VAL* 3.1 17.2 + - - +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.9 8.2 + - - +
129B TYR* 4.4 8.4 - - + -
130B LEU* 4.6 8.2 - - + +
133B LYS* 3.7 36.3 - - + -
136B SER* 3.0 20.7 + - - +
138B CYS* 1.3 78.3 - - - +
140B TRP* 1.3 62.0 + - - +
142B VAL* 3.2 20.3 + - - +
143B VAL* 3.3 17.6 + - - +
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Residues in contact with TRP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.1 4.3 - - + -
67B PHE* 5.6 3.1 - + - -
69B THR* 5.0 0.7 - - - -
71B ASP* 4.1 4.3 - - + -
72B SER* 3.1 41.7 - - - -
75B ALA* 3.4 22.8 - - + +
76B TRP* 3.5 44.7 - + + -
130B LEU* 3.8 32.1 - - + -
135B TYR* 3.1 48.6 + + + +
136B SER 3.0 26.2 + - - -
137B PRO* 3.1 11.9 + - + +
139B ALA* 1.3 75.2 - - - +
141B GLU* 1.3 60.0 + - - +
143B VAL* 3.1 19.1 + - + +
144B ARG 2.8 24.1 + - - -
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 3.4 8.8 - - - +
23B LYS 5.8 0.4 - - - +
24B ILE* 3.5 35.7 - - + +
25B SER* 3.4 4.0 - - - -
26B LEU* 2.7 40.0 + - + +
76B TRP* 4.3 5.2 - - + -
137B PRO 3.2 6.1 + - - +
138B CYS* 3.1 16.5 + - - +
140B TRP* 1.3 76.9 - - - +
142B VAL* 1.3 56.2 + - - +
144B ARG* 2.6 54.0 + - - +
145B ALA* 2.8 30.3 + - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 5.5 2.9 - - - +
26B LEU* 3.7 14.1 - - + -
32B ASP* 3.6 33.9 - - + +
34B HIS 3.8 22.7 - - - +
35B ASP* 4.5 6.7 - - + -
36B PHE* 3.9 17.3 - - + -
129B TYR* 4.6 6.3 - - + -
138B CYS 3.1 16.0 + - - +
139B ALA* 3.3 10.8 - - - +
141B GLU* 1.3 76.8 - - - +
143B VAL* 1.3 57.5 + - + +
145B ALA* 3.2 6.5 + - + +
146B GLU* 2.9 37.1 + - + +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 5.3 4.3 - - + -
66B LEU* 4.6 13.7 - - + -
67B PHE* 4.7 7.6 - - + -
76B TRP* 5.4 0.2 - - + -
126B ILE* 3.7 32.8 - - + -
129B TYR* 5.5 2.2 - - + -
130B LEU* 3.8 20.9 - - + -
139B ALA 3.3 15.5 - - - +
140B TRP* 3.1 18.6 + - + +
142B VAL* 1.3 78.6 - - + +
144B ARG* 1.3 57.3 + - - +
146B GLU* 3.2 6.8 + - - +
147B ILE* 2.8 51.0 + - + +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 3.7 22.8 - - - +
18B LEU* 3.5 35.7 - - + +
19B ALA* 4.8 1.9 - - - +
22B ARG* 3.3 32.2 - - + +
26B LEU* 4.6 4.4 - - - +
67B PHE* 5.6 1.8 - - + -
76B TRP* 4.1 15.7 - - + -
140B TRP 2.8 11.6 + - - +
141B GLU* 2.6 50.9 + - - +
143B VAL* 1.3 78.1 - - - +
145B ALA* 1.3 62.2 + - - +
147B ILE* 3.8 4.3 - - - +
148B MET* 2.8 72.8 + - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 3.8 24.2 - - + +
47A SER* 6.1 2.0 - - - +
26B LEU* 4.2 18.2 - - + -
141B GLU 2.8 19.5 + - - +
142B VAL* 3.5 4.9 - - - +
144B ARG* 1.3 86.6 - - - +
146B GLU* 1.3 59.4 + - + +
148B MET* 3.7 1.8 - - - +
149B ARG* 2.9 34.7 + - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 6.0 0.5 - - - -
35B ASP* 3.6 11.4 - - - +
36B PHE* 2.7 43.5 + - + +
37B GLY* 2.8 28.1 + - - -
38B PHE* 3.8 2.6 + - - +
122B TYR* 2.6 28.9 + - - +
126B ILE* 4.8 4.5 - - + -
142B VAL* 2.9 23.7 + - + +
143B VAL* 3.2 6.3 + - - +
145B ALA* 1.3 77.1 - - + +
147B ILE* 1.3 50.7 + - - +
149B ARG* 3.1 7.1 + - - +
150B SER* 2.7 40.4 + - - -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.8 31.2 - - + -
63B ILE* 4.4 11.4 - - + -
66B LEU* 5.3 0.7 - - + -
67B PHE* 4.3 13.2 - - + -
122B TYR* 4.6 0.9 - - + -
123B PHE* 3.7 34.5 - - + -
126B ILE* 4.3 17.5 - - + -
143B VAL* 2.8 37.2 + - + +
144B ARG 3.9 2.0 - - - +
146B GLU* 1.3 73.1 - - - +
148B MET* 1.3 63.7 + - - +
150B SER* 3.1 12.0 + - - +
151B PHE* 3.0 34.5 + - + -
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Residues in contact with MET 148 (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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46A MET* 4.8 7.4 - - + -
15B LEU* 4.0 34.4 - - + +
18B LEU* 4.6 13.4 - - + +
19B ALA* 5.0 13.9 - - + -
144B ARG* 2.8 55.4 + - - +
145B ALA 3.7 4.0 - - - +
147B ILE* 1.3 73.2 - - - +
149B ARG* 1.3 65.4 + - - +
151B PHE* 3.4 5.5 + - - +
152B SER* 2.9 26.3 + - - +
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Residues in contact with ARG 149 (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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46A MET* 3.4 28.3 - - - -
76A HIS* 2.8 58.9 + - + +
77A GLU* 3.0 30.9 + - + +
78A ALA 3.7 0.4 - - - +
100A TRP* 3.5 21.9 - - - -
38B PHE* 5.1 2.0 - - + -
145B ALA 2.9 20.8 + - - +
146B GLU* 3.5 6.3 - - - +
148B MET* 1.3 81.8 - - - +
150B SER* 1.3 65.0 + - - +
152B SER* 3.1 14.4 + - - -
153B LEU* 3.0 33.4 + - + +
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Residues in contact with SER 150 (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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38B PHE* 3.2 42.4 - - - +
59B MET* 3.9 10.1 - - - -
122B TYR* 3.2 16.3 + - - -
123B PHE* 6.1 0.2 - - - -
146B GLU 2.7 24.9 + - - -
147B ILE* 3.1 15.5 + - - -
149B ARG* 1.3 73.1 - - - +
151B PHE* 1.3 51.8 + - - +
153B LEU* 2.9 16.3 + - - +
154B SER* 2.6 26.1 + - - -
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Residues in contact with PHE 151 (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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11B SER* 4.6 17.3 - - - +
14B THR* 3.9 31.2 - - + -
15B LEU* 4.0 17.7 - - + -
18B LEU* 3.7 26.0 - - + -
56B LEU* 5.7 1.6 - - + -
59B MET* 4.8 5.6 - - + -
60B ILE* 4.7 18.4 - - + -
63B ILE* 3.6 33.0 - - + -
88B LEU* 5.2 0.7 - - + -
91B GLN* 5.9 0.9 - - + -
147B ILE* 3.0 24.1 + - + -
148B MET 3.7 8.3 - - - +
150B SER* 1.3 75.9 - - - +
152B SER* 1.3 60.8 + - - +
153B LEU 3.1 0.9 + - - -
154B SER* 3.1 11.6 + - - -
155B THR* 3.4 23.5 + - + -
156B ASN* 3.2 24.0 + - - +
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 3.5 27.9 - - - -
15B LEU* 3.8 13.3 - - - +
148B MET* 2.9 17.5 + - - +
149B ARG* 3.1 17.3 + - - -
151B PHE* 1.3 76.4 - - - +
153B LEU* 1.3 59.1 + - - +
154B SER 3.6 0.2 - - - -
156B ASN* 2.9 35.2 + - - +
157B LEU* 3.9 3.8 - - - +
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Residues in contact with LEU 153 (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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76A HIS* 3.6 34.1 - - + +
38B PHE* 3.6 39.8 - - + +
40B GLN* 3.5 44.3 - - + +
43B PHE* 4.1 5.4 - - - +
44B GLY 4.2 0.3 + - - -
149B ARG* 3.0 21.5 + - + +
150B SER 2.9 3.4 + - - -
152B SER* 1.3 80.6 - - - +
154B SER* 1.3 56.5 + - - +
157B LEU* 3.7 23.5 - - + +
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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