Contacts of the helix formed by residues 31 - 49 (chain B) in PDB entry 6GHM
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 THR 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 4.8 0.4 - - - +
30B LEU* 1.3 73.5 - - - +
32B GLU* 1.3 70.5 + - - +
33B ASN* 2.6 30.5 + - + +
34B GLU* 3.0 46.9 + - + +
35B ILE* 3.0 23.9 + - - +
144B TYR* 4.2 2.9 - - - -
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Residues in contact with GLU 32 (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 THR* 1.3 75.1 + - - +
33B ASN* 1.3 67.8 + - - +
35B ILE* 3.3 6.3 + - - +
36B ARG* 2.9 53.0 + - - +
144B TYR* 3.8 25.3 - - + -
145B ASN* 3.1 31.4 + - - +
147B LYS* 6.0 0.9 - - - +
148B LEU* 4.4 15.2 - - + +
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 2.6 29.6 + - + -
32B GLU* 1.3 78.4 + - - +
34B GLU* 1.3 63.8 + - + +
36B ARG* 3.4 20.1 + - - +
37B GLY* 3.0 18.2 + - - -
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 6.6 0.4 - - - -
8B ASN* 6.2 1.5 - - - +
12B ILE* 3.8 23.9 - - + +
15B ARG* 2.9 44.3 + - - -
30B LEU* 3.5 8.7 - - + +
31B THR* 3.0 39.0 + - + +
33B ASN* 1.3 73.2 - - + +
35B ILE* 1.3 67.1 + - - +
37B GLY* 3.0 4.0 + - - -
38B LEU* 3.0 25.9 + - - +
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Residues in contact with ILE 35 (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 LEU* 4.0 15.0 - - + -
31B THR 3.0 11.0 + - - +
32B GLU 3.8 3.6 - - - +
34B GLU* 1.3 76.5 - - - +
36B ARG* 1.3 62.3 + - - +
38B LEU* 3.2 10.9 + - + +
39B CYS* 3.0 23.0 + - - -
101B LEU* 5.0 4.7 - - + -
105B CYS* 4.0 20.9 - - - -
144B TYR* 3.4 44.9 - - + +
148B LEU* 3.8 18.8 - - + -
152B PHE* 3.4 35.7 - - + -
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Residues in contact with ARG 36 (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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32B GLU* 2.9 53.6 + - - +
33B ASN* 3.6 29.6 - - - +
35B ILE* 1.3 78.2 - - - +
37B GLY* 1.3 57.0 + - - +
39B CYS* 3.3 0.7 + - - +
40B LEU* 2.9 52.1 + - + +
147B LYS* 5.8 7.7 - - - +
148B LEU* 4.5 7.0 - - + +
151B THR* 4.2 30.6 + - + +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 6.5 0.9 - - - -
33B ASN 3.0 10.2 + - - -
34B GLU* 3.0 8.6 + - - -
36B ARG* 1.3 76.8 - - - +
38B LEU* 1.3 62.1 + - - +
40B LEU* 4.8 4.0 - - - -
41B LYS* 2.9 30.3 + - - +
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Residues in contact with LEU 38 (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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9B LEU* 3.8 20.4 - - + -
12B ILE* 4.1 25.8 - - + -
30B LEU* 4.4 3.8 - - + -
34B GLU 3.0 17.6 + - - +
35B ILE* 3.2 10.7 + - + +
37B GLY* 1.3 77.0 - - - +
39B CYS* 1.3 51.8 + - - +
42B SER* 2.7 41.0 + - - -
105B CYS* 3.8 41.1 - - + +
108B LEU* 4.3 14.4 - - + -
109B ALA* 4.0 11.9 - - + -
112B ILE* 3.6 21.5 - - + +
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Residues in contact with CYS 39 (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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35B ILE* 3.0 20.7 + - - +
36B ARG 3.3 0.9 + - - +
38B LEU* 1.3 76.6 - - - +
40B LEU* 1.3 59.0 + - + +
42B SER* 3.3 6.0 + - - -
43B ARG* 3.0 32.1 + - - +
108B LEU* 4.2 4.7 - - - -
151B THR* 3.5 37.5 - - + +
152B PHE* 3.5 47.3 - - - -
155B CYS* 3.7 10.3 - - + +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 2.9 38.4 + - + +
37B GLY* 4.2 3.6 - - - +
39B CYS* 1.3 75.4 - - + +
41B LYS* 1.3 63.6 + - - +
43B ARG* 3.4 16.7 + - - +
44B GLU* 3.2 31.7 + - - +
151B THR* 4.9 12.1 - - + -
154B ASP* 6.5 1.3 - - + -
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Residues in contact with LYS 41 (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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7B LEU* 5.8 11.2 - - + -
37B GLY 2.9 18.8 + - - +
40B LEU* 1.3 78.4 - - - +
42B SER* 1.3 62.0 + - - +
44B GLU* 3.3 12.7 + - - +
45B ILE* 3.3 22.9 + - + +
112B ILE* 3.6 35.9 - - + -
401B EDO 3.2 35.2 + - - -
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Residues in contact with SER 42 (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 LEU 2.7 23.9 + - - -
39B CYS 3.3 4.3 + - - -
41B LYS* 1.3 78.0 - - - +
43B ARG* 1.3 59.1 + - - +
45B ILE* 3.0 8.3 + - - +
46B PHE* 2.9 46.6 + - - -
108B LEU* 3.4 16.6 - - - +
111B LYS* 4.8 3.6 - - - -
112B ILE* 3.9 19.2 - - - +
155B CYS* 3.3 15.6 - - - -
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Residues in contact with ARG 43 (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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39B CYS 3.0 19.7 + - - +
40B LEU* 3.5 18.4 - - - +
41B LYS 3.3 0.2 - - - -
42B SER* 1.3 77.1 + - - +
44B GLU* 1.3 66.9 + - + +
46B PHE* 3.3 13.0 + - - +
47B LEU* 3.0 38.8 + - + +
154B ASP* 3.4 32.3 + - - +
155B CYS* 4.2 6.3 - - - +
158B CYS* 3.5 21.1 - - + -
192B PRO* 3.6 31.9 - - - +
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Residues in contact with GLU 44 (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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40B LEU* 3.2 16.7 + - - +
41B LYS* 3.6 16.8 + - - +
43B ARG* 1.3 81.6 - - + +
45B ILE* 1.3 61.5 + - - +
47B LEU* 3.5 7.1 + - - +
48B SER* 3.1 23.6 + - - -
401B EDO 2.7 36.0 + - - +
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Residues in contact with ILE 45 (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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41B LYS* 3.3 20.8 + - - +
42B SER* 3.0 9.4 + - - +
44B GLU* 1.3 74.4 - - - +
46B PHE* 1.3 65.7 + - - +
48B SER* 2.9 23.0 + - - +
49B GLN* 3.1 18.5 + - - +
111B LYS* 3.8 28.9 - - + +
112B ILE* 3.8 41.1 - - + +
115B PRO* 3.9 21.3 - - + -
401B EDO 3.6 21.3 - - - -
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Residues in contact with PHE 46 (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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42B SER* 2.9 26.8 + - - -
43B ARG* 3.3 9.8 + - - +
45B ILE* 1.3 75.3 - - - +
47B LEU* 1.3 57.4 + - - +
49B GLN* 2.9 31.0 + - - +
50B PRO 4.8 0.2 - - - +
108B LEU* 4.0 15.3 - - + -
111B LYS* 3.6 42.0 - - + -
120B LEU* 4.0 11.4 - - + -
155B CYS* 3.8 30.7 - - - -
158B CYS* 3.3 21.5 - - + +
159B LEU* 3.5 30.3 - - + -
160B PRO* 4.1 15.2 - - + +
191B ARG* 3.1 11.1 + - - +
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Residues in contact with LEU 47 (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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43B ARG* 3.0 46.1 + - + +
44B GLU* 4.0 6.5 - - - +
46B PHE* 1.3 75.5 - - - +
48B SER* 1.3 60.8 + - - +
49B GLN 3.5 2.1 + - - +
158B CYS* 3.8 21.8 - - + -
191B ARG* 3.6 37.0 - - + +
192B PRO* 5.1 4.0 - - + -
402B EDO 3.3 40.6 + - - -
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Residues in contact with SER 48 (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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44B GLU 3.1 15.3 + - - -
45B ILE* 2.9 17.5 + - - +
47B LEU* 1.3 76.3 - - - +
49B GLN* 1.3 64.7 + - - +
50B PRO* 4.6 1.0 - - - +
401B EDO 3.7 17.0 + - - -
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Residues in contact with GLN 49 (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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45B ILE* 3.1 17.7 + - + +
46B PHE* 2.9 20.4 + - - +
47B LEU 3.7 1.9 - - - +
48B SER* 1.3 86.2 - - - +
50B PRO* 1.3 73.7 - - + +
53B LEU* 4.4 7.9 - - + +
111B LYS* 2.8 26.8 + - - -
115B PRO* 2.8 31.1 + - - +
116B GLU* 3.6 22.7 + - - +
119B PHE* 3.9 12.4 - - - -
160B PRO* 6.5 0.2 - - + -
191B ARG* 2.9 13.9 + - - -
402B EDO 4.7 0.3 + - - -
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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
------------------------------------------------------------
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