Contacts of the helix formed by residues 28 - 40 (chain G) in PDB entry 5B31
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 28 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G SER* 3.3 6.5 - - - +
26G GLN 3.8 0.4 - - - -
27G PHE* 1.3 92.4 - - + +
29G VAL* 1.3 64.8 + - - +
30G GLY 3.2 2.5 - - - +
31G ARG* 3.2 25.8 + - + +
32G ILE* 3.1 23.6 + - + +
37H TYR* 4.3 8.3 - - + -
40H TYR* 3.5 48.9 - - + +
176J A 5.4 2.0 - - - +
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Residues in contact with VAL 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG* 3.6 46.4 - - + +
20G SER* 2.9 29.8 + - - +
23G ALA* 5.0 0.7 - - + -
25G LEU* 4.1 10.5 - - + -
27G PHE 3.2 2.6 + - - +
28G PRO* 1.3 71.8 - - - +
30G GLY* 1.3 62.3 + - - +
32G ILE* 3.4 2.0 + - - -
33G HIS* 3.0 22.5 + - - +
51G ALA* 3.7 13.3 - - + +
52G VAL* 4.0 17.5 - - + +
55G ALA* 3.8 25.6 - - + -
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Residues in contact with GLY 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG* 4.8 3.1 - - - -
20G SER* 4.8 0.6 + - - +
28G PRO* 3.2 1.4 - - - +
29G VAL* 1.3 80.1 - - - +
31G ARG* 1.3 61.6 + - - +
33G HIS* 3.5 5.9 + - - +
34G ARG* 3.2 17.0 + - - +
176J A 3.5 37.3 + - - +
177J G 4.3 12.8 + - - -
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Residues in contact with ARG 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G PRO* 3.2 24.8 + - + +
30G GLY* 1.3 73.9 - - - +
32G ILE* 1.3 61.9 + - - +
34G ARG* 3.0 19.3 + - - +
35G HIS* 2.9 54.5 + - + +
35H GLU* 3.5 21.0 + - - +
36H SER 2.8 34.2 + - - +
37H TYR* 4.4 11.4 - - - +
40H TYR* 3.7 16.8 + - - -
121I G 3.4 21.4 + - - -
122I G 3.3 17.7 + - - -
176J A 3.6 26.5 + - - +
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Residues in contact with ILE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PHE* 4.5 4.3 - - + -
28G PRO* 3.1 26.0 + - + +
29G VAL 4.0 3.1 - - - +
30G GLY 3.4 0.2 - - - -
31G ARG* 1.3 77.9 - - + +
33G HIS* 1.3 57.1 + - - +
35G HIS* 3.4 7.0 + - - +
36G LEU* 2.9 29.4 + - + +
51G ALA* 3.8 22.7 - - - +
54G SER* 3.9 11.4 - - - -
55G ALA* 3.5 31.0 - - + -
58G LEU* 3.9 17.5 - - + -
37H TYR* 4.1 20.6 - - + +
70H PHE* 3.7 20.6 - - + -
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Residues in contact with HIS 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG* 2.9 34.7 + - - +
29G VAL 3.0 11.8 + - - +
30G GLY 3.5 5.4 - - - +
31G ARG 3.2 0.2 - - - -
32G ILE* 1.3 79.1 - - - +
34G ARG* 1.3 57.6 + - - +
36G LEU* 3.1 5.9 + - - +
37G LYS* 2.8 40.8 + - + +
46G VAL* 4.0 24.4 + - + +
47G GLY 3.8 21.1 + - - -
48G ALA* 5.0 2.7 - - - -
51G ALA* 3.5 18.2 - - + +
112I T 4.6 8.1 + - - -
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Residues in contact with ARG 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G GLY 3.2 8.5 + - - +
31G ARG* 3.0 28.3 + - - +
33G HIS* 1.3 79.9 - - - +
35G HIS* 1.3 76.3 + - - +
37G LYS* 3.2 9.3 + - + +
38G SER* 2.9 27.3 + - - -
35H GLU* 2.8 45.7 + - - -
175J A 3.7 21.9 + - - -
176J A 3.2 27.5 + - - +
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Residues in contact with HIS 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ARG* 2.9 39.0 + - + +
32G ILE* 3.7 5.1 - - - +
34G ARG* 1.3 101.9 + - - +
36G LEU* 1.3 63.6 + - - +
38G SER* 3.1 9.2 + - - +
39G ARG* 3.1 21.0 + - - +
35H GLU* 3.4 8.1 + - + -
37H TYR* 3.7 22.1 + + - -
67H ASN* 5.8 1.1 - - - -
70H PHE* 3.7 28.0 - + + -
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Residues in contact with LEU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G ILE* 2.9 23.7 + - + +
33G HIS 3.1 3.8 + - - +
35G HIS* 1.3 76.3 - - - +
37G LYS* 1.3 62.4 + - - +
39G ARG* 3.2 6.4 + - - +
40G THR* 3.1 26.3 + - - +
46G VAL* 4.0 29.4 - - + +
50G ALA* 4.2 5.4 - - + +
51G ALA* 4.1 22.9 - - + +
54G SER* 4.1 16.8 - - - +
70H PHE* 3.7 20.4 - - + -
74H ALA* 3.8 24.7 - - + -
89H ILE* 4.7 19.2 - - + +
94H ILE* 5.0 3.1 - - + -
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Residues in contact with LYS 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G HIS* 2.8 28.2 + - + +
34G ARG* 3.4 9.9 - - + +
36G LEU* 1.3 79.2 - - - +
38G SER* 1.3 52.4 + - - +
40G THR* 2.5 33.8 - - + +
41G THR* 3.2 15.8 + - - +
42G SER* 3.9 10.9 + - - +
44G GLY 3.0 26.8 + - - -
46G VAL* 4.0 8.9 - - + +
112I T 3.1 40.2 + - - -
113I A 5.3 1.2 + - - -
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Residues in contact with SER 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D HIS* 4.4 18.7 + - - -
34G ARG* 2.9 13.0 + - - -
35G HIS* 3.1 13.4 + - - -
37G LYS* 1.3 73.4 - - - +
39G ARG* 1.3 58.6 + - - +
40G THR 2.8 14.0 - - - +
41G THR* 4.4 6.5 - - - +
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Residues in contact with ARG 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN 3.6 15.6 - - - +
39C TYR 5.3 1.6 - - - +
79D ARG* 6.1 1.8 - - - +
35G HIS 3.1 12.8 + - - +
36G LEU* 3.2 9.4 + - - +
38G SER* 1.3 76.0 - - - +
40G THR* 1.3 65.9 + - - +
41G THR* 4.3 0.7 - - - +
70H PHE* 6.0 2.0 - - + -
71H GLU* 2.7 39.0 + - - -
74H ALA* 3.5 38.5 - - + +
75H GLY* 3.7 13.7 + - - -
78H SER* 3.7 26.8 + - - +
79H ARG* 5.9 0.2 - - - +
89H ILE* 4.7 7.2 - - + -
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Residues in contact with THR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 4.6 9.2 + - - -
36G LEU 3.1 15.9 + - - +
37G LYS* 2.5 25.9 - - + +
38G SER 2.8 6.6 - - - +
39G ARG* 1.3 87.2 - - - +
41G THR* 1.3 67.5 + - - +
44G GLY* 3.3 28.2 - - - -
45G ARG 3.6 4.3 + - - +
46G VAL* 3.8 20.0 - - + -
78H SER* 6.2 0.2 - - - -
82H HIS* 5.8 2.6 - - - -
87H SER 3.9 5.5 + - - -
89H ILE* 4.6 16.3 - - - +
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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
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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