Contacts of the helix formed by residues 37 - 55 (chain B) in PDB entry 4RUH
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 LYS 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B GLN* 2.7 60.5 + - + +
31B VAL* 4.0 10.1 - - + +
34B TRP* 3.0 42.7 + - + +
36B GLU* 1.3 88.6 - - + +
38B ARG* 1.3 57.2 + - - +
39B GLY 3.3 2.7 - - - -
40B GLU* 3.0 34.8 + - + +
41B ILE* 3.2 11.2 + - - +
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Residues in contact with ARG 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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32B SER* 3.3 26.7 + - - +
34B TRP 4.0 3.4 + - - -
35B PRO* 3.3 20.4 + - - +
36B GLU 3.1 2.8 - - - -
37B LYS* 1.3 78.7 - - - +
39B GLY* 1.3 59.9 + - - +
41B ILE* 3.5 12.2 + - - +
42B ARG* 3.4 26.0 + - - +
67B GLN* 2.9 25.4 + - - -
75B ILE* 3.3 25.6 + - + +
76B PRO* 2.5 66.8 + - + +
77B LEU* 3.9 9.9 - - - +
78B PRO* 4.0 21.1 - - - +
165B MET* 4.1 11.9 - - - +
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU 4.7 2.2 + - - -
37B LYS 3.3 0.6 - - - -
38B ARG* 1.3 76.3 - - - +
40B GLU* 1.3 62.5 + - - +
41B ILE 3.3 0.2 - - - -
42B ARG* 3.9 25.3 - - - +
43B ARG* 3.1 25.4 + - - +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA 5.2 0.2 - - - +
28B ILE* 3.4 19.9 - - + +
29B GLN* 3.3 39.0 + - + +
30B SER* 4.5 0.9 - - - -
36B GLU 5.6 0.7 - - - +
37B LYS* 3.0 29.6 + - + +
39B GLY* 1.3 78.3 - - - +
41B ILE* 1.3 58.1 + - - +
43B ARG* 3.1 40.7 + - - +
44B MET* 2.9 21.7 + - - +
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Residues in contact with ILE 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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30B SER* 3.1 31.4 - - - +
31B VAL 3.8 2.5 - - - +
32B SER* 3.4 44.2 - - - +
37B LYS 3.2 13.7 + - - +
38B ARG* 3.7 21.1 - - - +
39B GLY 3.3 0.2 - - - -
40B GLU* 1.3 72.9 - - - +
42B ARG* 1.3 58.2 + - - +
43B ARG 2.9 1.1 - - - -
44B MET* 2.7 23.6 + - - +
45B MET* 3.0 18.0 + - - +
78B PRO* 3.5 23.6 - - + -
101B ASP* 4.3 0.9 - - + +
164B GLY* 3.6 20.0 - - - +
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Residues in contact with ARG 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 ARG* 3.4 21.5 + - - +
39B GLY* 3.9 17.8 - - - +
41B ILE* 1.3 77.1 - - - +
43B ARG* 1.3 61.5 + - - +
45B MET* 3.3 11.1 + - - +
46B GLU* 3.3 28.4 + - + +
61B LEU* 6.3 0.4 - - + -
76B PRO* 4.4 23.5 - - - +
77B LEU 4.9 8.1 + - - -
78B PRO* 4.2 2.2 - - + +
79B PRO* 3.6 35.2 - - + +
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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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28B ILE* 3.7 38.0 - - - +
39B GLY 3.1 17.3 + - - +
40B GLU* 3.1 47.4 + - - +
41B ILE 2.9 0.8 - - - -
42B ARG* 1.3 77.4 - - - +
44B MET* 1.3 54.5 + - - +
46B GLU* 3.0 41.0 + - - +
47B VAL* 3.3 14.9 - - + +
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Residues in contact with MET 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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25B TRP* 3.4 69.5 - - + +
28B ILE* 3.9 21.8 - - + -
30B SER* 4.1 9.0 - - - +
40B GLU 2.9 11.6 + - - +
41B ILE 2.7 13.6 + - - +
43B ARG* 1.3 72.3 - - - +
45B MET* 1.3 61.0 + - - +
47B VAL* 3.7 11.7 + - + -
48B ALA* 3.3 13.9 + - - +
100B LEU* 3.7 36.6 - - + +
134B LYS* 4.3 6.5 - - - -
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Residues in contact with MET 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 ILE* 3.0 17.2 + - - +
42B ARG* 3.5 14.4 - - - +
43B ARG 3.1 0.2 - - - -
44B MET* 1.3 76.0 - - - +
46B GLU* 1.3 60.4 + - - +
48B ALA* 3.4 6.0 + - - +
49B ALA* 2.8 28.2 + - - +
61B LEU* 4.2 7.3 - - + +
78B PRO* 4.7 2.0 - - + -
79B PRO* 3.5 35.2 - - + +
81B LEU* 3.6 14.7 - - + +
100B LEU* 3.7 24.9 - - + -
162B LEU 3.4 29.6 - - - +
163B GLU 3.6 22.0 - - - +
164B GLY* 4.2 7.2 - - - -
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Residues in contact with GLU 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 ARG* 3.3 24.4 - - + +
43B ARG* 3.0 22.1 + - - +
45B MET* 1.3 75.9 - - - +
47B VAL* 1.3 56.0 - - + +
49B ALA* 3.0 8.1 + - - +
50B ALA* 2.8 36.7 + - - +
61B LEU* 4.4 15.6 - - + +
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Residues in contact with VAL 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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21B LYS* 6.0 0.9 - - - +
25B TRP* 4.3 22.2 - - + +
28B ILE* 4.1 23.6 - - + -
43B ARG* 3.3 20.2 - - + +
44B MET* 3.9 11.4 - - + +
46B GLU* 1.3 75.4 - - + +
48B ALA* 1.3 62.0 + - - +
50B ALA* 3.5 7.8 + - + +
51B ASP* 3.3 27.7 + - - +
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Residues in contact with ALA 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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25B TRP* 5.0 9.9 - - + -
44B MET* 3.3 7.2 + - + +
45B MET 3.6 6.7 - - - +
46B GLU 3.1 0.6 - - - -
47B VAL* 1.3 78.4 - - - +
49B ALA* 1.3 63.9 + - - +
51B ASP* 3.2 20.3 + - - +
52B VAL* 3.4 14.0 + - - +
81B LEU* 3.6 11.4 - - + +
100B LEU* 3.6 33.7 - - + -
141B ILE* 5.3 1.3 - - + +
162B LEU* 4.2 8.5 - - + -
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Residues in contact with ALA 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 MET 2.8 17.6 + - - +
46B GLU* 3.4 9.0 - - - +
48B ALA* 1.3 75.8 - - - +
50B ALA* 1.3 62.4 + - - +
51B ASP 3.3 0.5 + - - -
52B VAL* 3.4 7.3 + - - +
53B LYS* 3.2 21.9 - - + +
59B VAL* 3.5 31.2 - - + +
61B LEU* 4.3 13.9 - - + -
81B LEU* 3.4 9.4 - - + +
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Residues in contact with ALA 50 (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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46B GLU 2.8 15.5 + - - +
47B VAL* 3.7 10.1 - - + +
49B ALA* 1.3 77.9 - - - +
51B ASP* 1.3 60.1 + - - +
53B LYS* 3.4 12.7 + - - +
54B GLN* 3.0 27.9 + - - +
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Residues in contact with ASP 51 (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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21B LYS* 3.2 37.5 + - - -
25B TRP* 3.9 11.9 - - - -
47B VAL* 3.3 17.3 + - - +
48B ALA* 3.2 13.0 + - - +
49B ALA 3.2 0.4 - - - -
50B ALA* 1.3 79.7 - - - +
52B VAL* 1.3 59.9 + - - +
54B GLN* 3.1 14.4 + - - +
55B LEU* 3.0 31.7 + - - +
141B ILE* 3.4 24.5 - - + +
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Residues in contact with VAL 52 (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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48B ALA 3.6 14.8 - - - +
49B ALA* 3.4 7.7 + - - +
50B ALA 3.3 0.2 - - - -
51B ASP* 1.3 77.6 - - - +
53B LYS* 1.3 52.5 + - - +
55B LEU* 3.1 17.8 + - + +
56B GLY 3.3 0.2 + - - -
57B GLY* 2.7 42.6 + - - -
58B SER 4.1 14.4 - - - +
59B VAL* 4.8 7.0 - - + -
81B LEU* 5.0 7.9 - - + -
83B GLY* 4.7 3.1 - - - -
84B ARG 4.2 5.4 - - - +
85B LEU* 4.8 3.6 - - + -
141B ILE* 4.4 9.2 - - + -
160B PHE* 4.0 43.3 - - + -
162B LEU* 6.0 1.6 - - + -
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Residues in contact with LYS 53 (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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49B ALA* 3.2 17.9 - - + +
50B ALA* 3.4 11.6 + - - +
51B ASP 3.2 0.4 - - - -
52B VAL* 1.3 73.6 - - - +
54B GLN* 1.3 65.7 + - - +
55B LEU 3.1 0.4 - - - -
56B GLY* 3.0 12.6 + - - -
57B GLY 3.5 16.8 - - - +
58B SER* 5.0 1.3 - - - +
59B VAL* 3.6 22.0 - - + -
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Residues in contact with GLN 54 (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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50B ALA* 3.0 16.3 + - - +
51B ASP* 3.1 20.7 + - - +
53B LYS* 1.3 78.0 - - - +
55B LEU* 1.3 63.4 + - + +
56B GLY* 3.1 1.3 + - - -
145B GLU* 5.7 4.5 - - - +
148B GLN* 3.9 6.4 - - - +
149B LYS* 5.4 7.1 + - - +
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Residues in contact with LEU 55 (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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51B ASP 3.0 16.3 + - - +
52B VAL* 3.1 12.7 + - - +
54B GLN* 1.3 81.4 - - + +
56B GLY* 1.3 58.4 + - - +
57B GLY 3.4 0.2 - - - -
85B LEU* 3.6 20.9 - - + +
141B ILE* 3.9 28.0 - - + +
144B LEU* 3.6 34.3 - - + -
145B GLU* 4.1 36.1 - - + +
148B GLN* 2.5 39.2 + - - +
149B LYS* 6.5 0.4 - - - -
160B PHE* 4.8 2.5 - - + -
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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
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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