Contacts of the helix formed by residues 37 - 55 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.0 51.5 + - + +
31A VAL 3.5 10.8 - - - +
34A TRP* 2.8 52.6 + - + +
36A GLU* 1.3 99.5 + - - +
38A ARG* 1.3 62.7 + - - +
39A GLY 3.3 2.5 - - - -
40A GLU* 3.1 20.0 + - + +
41A ILE* 3.2 13.7 + - - +
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.2 24.9 + - - +
34A TRP 3.9 3.0 + - - -
35A PRO* 3.3 20.3 + - - +
36A GLU 3.3 1.4 - - - -
37A LYS* 1.3 78.7 - - - +
39A GLY* 1.3 61.8 + - - +
41A ILE* 3.2 22.2 + - - +
42A ARG* 3.4 15.4 + - - +
67A GLN* 3.1 28.7 + - - +
75A ILE* 3.7 19.5 - - + +
76A PRO* 2.9 53.9 + - + +
77A LEU* 3.9 10.3 - - - +
78A PRO* 3.8 25.1 - - + +
165A MET* 3.9 14.3 - - - +
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Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU 4.7 2.6 + - - -
37A LYS 3.3 0.4 - - - -
38A ARG* 1.3 75.6 - - - +
40A GLU* 1.3 64.4 + - - +
42A ARG* 3.3 31.8 + - - +
43A ARG* 3.2 21.1 + - - +
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.4 16.5 - - + +
29A GLN* 3.3 33.0 - - + +
30A SER* 4.6 0.4 - - - -
36A GLU 5.5 0.2 + - - -
37A LYS* 3.1 21.3 + - + +
39A GLY* 1.3 77.6 - - - +
41A ILE* 1.3 60.8 + - - +
43A ARG* 3.4 5.7 + - - +
44A MET 3.2 16.8 + - - -
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER* 3.7 29.4 - - - +
31A VAL 4.0 3.1 - - - +
32A SER* 3.7 26.9 - - - +
37A LYS 3.2 10.9 + - - +
38A ARG* 3.2 29.2 + - - +
40A GLU* 1.3 76.1 - - - +
42A ARG* 1.3 57.5 + - - +
44A MET* 3.3 3.2 + - + +
45A MET* 3.0 31.7 + - + +
78A PRO* 3.4 24.7 - - + -
100A LEU 5.4 0.4 - - - -
101A ASP* 4.8 1.8 - - + +
164A GLY* 3.6 33.2 - - - +
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.4 9.1 + - - +
39A GLY* 3.3 30.6 + - - +
41A ILE* 1.3 77.7 - - - +
43A ARG* 1.3 60.4 + - - +
45A MET* 3.3 7.4 + - - +
46A GLU* 2.9 30.4 + - + +
61A LEU* 5.5 2.2 - - + +
76A PRO* 4.5 22.4 - - - +
77A LEU 5.8 1.2 + - - -
78A PRO* 4.9 3.7 - - + +
79A PRO* 4.2 24.7 - - + +
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.8 11.0 - - + -
39A GLY 3.2 10.2 + - - +
40A GLU* 3.4 11.4 + - - +
42A ARG* 1.3 77.1 - - - +
44A MET* 1.3 52.6 + - - +
46A GLU* 3.1 8.9 + - - +
47A VAL* 2.6 40.8 + - + +
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Residues in contact with MET 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TRP* 3.5 70.2 - - + +
28A ILE* 3.8 16.6 - - + +
30A SER* 4.4 3.6 - - - -
40A GLU 3.2 10.8 + - - +
41A ILE* 3.4 12.3 - - - +
43A ARG* 1.3 74.4 - - - +
45A MET* 1.3 65.2 + - - +
47A VAL* 3.2 16.4 + - + +
48A ALA 3.0 19.0 + - - +
100A LEU* 3.5 40.9 - - + +
134A LYS* 4.1 9.6 - - - -
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.0 27.8 + - + +
42A ARG* 3.3 6.0 + - - +
44A MET* 1.3 74.1 - - - +
46A GLU* 1.3 58.3 + - - +
48A ALA 3.3 1.6 + - - -
49A ALA* 2.9 29.8 + - - +
61A LEU* 4.2 14.1 - - + -
78A PRO* 4.6 0.7 - - + -
79A PRO* 3.8 28.5 - - + +
81A LEU* 3.6 22.0 - - + +
100A LEU* 3.5 28.5 - - + -
162A LEU* 3.3 33.9 - - + +
163A GLU 3.8 17.7 - - - +
164A GLY* 4.2 4.9 - - - -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 2.9 15.4 + - + +
43A ARG* 3.2 12.8 - - - +
45A MET* 1.3 76.1 - - - +
47A VAL* 1.3 62.3 + - - +
49A ALA* 3.2 8.1 + - - +
50A ALA* 2.9 24.6 + - - +
61A LEU* 4.4 13.3 - - + +
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 5.6 0.4 - - - +
24A LYS* 6.1 3.8 - - + -
25A TRP* 3.7 29.6 - - + +
28A ILE* 3.7 25.1 - - + -
43A ARG* 2.6 24.9 + - + +
44A MET* 3.3 13.9 - - + +
46A GLU* 1.3 74.2 - - - +
48A ALA* 1.3 63.4 + - - +
50A ALA* 3.2 8.1 + - - +
51A ASP* 3.2 21.0 + - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TRP* 4.6 15.9 - - + -
44A MET* 3.0 7.7 + - + +
47A VAL* 1.3 75.4 - - - +
49A ALA* 1.3 63.2 + - - +
51A ASP* 3.3 11.9 + - - +
52A VAL* 3.1 26.9 + - - +
81A LEU* 3.7 13.7 - - + -
100A LEU* 3.7 29.2 - - + -
137A VAL* 5.8 0.2 - - + -
141A ILE* 5.3 3.0 - - + +
162A LEU* 4.4 9.4 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET 2.9 17.1 + - - +
46A GLU* 3.2 9.8 + - - +
48A ALA* 1.3 74.2 - - - +
50A ALA* 1.3 64.4 + - - +
52A VAL* 3.4 1.7 + - - +
53A LYS* 3.1 28.2 + - + +
59A VAL* 3.5 27.9 - - + +
61A LEU* 4.3 13.5 - - + -
81A LEU* 3.5 10.7 - - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU 2.9 12.9 + - - +
47A VAL* 3.5 11.4 - - - +
49A ALA* 1.3 78.5 - - - +
51A ASP* 1.3 60.7 + - - +
53A LYS* 3.4 9.9 + - - +
54A GLN* 3.0 24.9 + - - +
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 2.5 37.3 + - - -
25A TRP* 3.4 13.5 + - - -
47A VAL* 3.2 14.2 + - - +
48A ALA* 3.4 11.7 - - - +
49A ALA 3.2 0.4 - - - -
50A ALA* 1.3 77.4 - - - +
52A VAL* 1.3 62.0 + - - +
54A GLN* 3.2 10.7 + - - +
55A LEU* 3.1 27.3 + - - +
141A ILE* 4.1 21.1 - - + +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA 3.1 15.0 + - - +
49A ALA* 3.8 5.4 - - - +
50A ALA 3.3 0.4 - - - -
51A ASP* 1.3 73.7 - - - +
53A LYS* 1.3 66.0 + - - +
55A LEU* 3.2 14.8 + - + +
56A GLY 3.4 0.2 + - - -
57A GLY* 3.0 31.2 + - - -
58A SER 4.5 0.2 - - - +
59A VAL* 4.2 22.4 - - + -
81A LEU* 4.7 7.6 - - + -
83A GLY* 4.2 14.1 - - - -
84A ARG 5.1 0.7 - - - +
85A LEU* 5.1 3.8 - - + -
141A ILE* 4.4 8.1 - - + -
160A PHE* 3.6 42.4 - - + -
162A LEU* 5.4 1.8 - - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 3.1 13.5 + - - +
50A ALA* 3.6 11.9 - - - +
51A ASP 3.3 0.2 - - - -
52A VAL* 1.3 77.0 - - - +
54A GLN* 1.3 57.4 + - - +
56A GLY* 2.8 21.8 + - - -
57A GLY 3.7 16.7 + - - +
58A SER* 5.6 2.2 - - - +
59A VAL* 3.4 26.2 - - + +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA 3.0 15.6 + - - +
51A ASP* 3.2 14.1 + - - +
53A LYS* 1.3 73.6 - - - +
55A LEU* 1.3 65.4 + - + +
56A GLY* 3.0 7.0 + - - -
148A GLN* 4.3 4.2 - - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP 3.1 16.8 + - - +
52A VAL* 3.5 13.2 - - - +
53A LYS 3.2 0.6 - - - -
54A GLN* 1.3 79.4 - - + +
56A GLY* 1.3 58.3 + - - +
57A GLY 3.5 0.2 - - - -
85A LEU* 3.7 23.6 - - + +
141A ILE* 4.3 24.2 - - + +
144A LEU* 3.7 39.0 - - + -
145A GLU* 4.1 28.9 - - + +
148A GLN* 2.8 42.7 + - - +
154A ILE* 5.1 0.4 - - + -
160A PHE* 4.9 0.7 - - + -
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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