Contacts of the helix formed by residues 24 - 38 (chain G) in PDB entry 6RI7
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 GLU 24 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G TYR* 2.7 24.7 + - + +
23G ARG* 1.3 76.0 - - + +
25G GLU* 1.3 64.1 + - - +
26G ARG 3.4 1.3 - - - -
27G PRO* 3.3 13.3 - - - +
28G GLU* 3.5 12.1 + - - +
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Residues in contact with GLU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G TYR 3.4 1.4 + - - +
21G LEU* 3.2 19.9 + - + +
24G GLU* 1.3 80.0 - - - +
26G ARG* 1.3 64.4 + - - +
27G PRO 3.3 0.3 - - - -
28G GLU* 3.4 3.8 + - - +
29G VAL* 2.9 24.7 + - - +
58G ILE* 6.5 0.4 - - + -
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Residues in contact with ARG 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ILE* 5.7 5.2 - - + -
21G LEU 3.0 15.9 + - - +
22G TRP* 4.1 16.8 - - - +
24G GLU 3.4 0.2 - - - -
25G GLU* 1.3 77.2 - - - +
27G PRO* 1.3 56.4 - - - +
29G VAL* 3.3 8.1 + - - +
30G THR* 2.9 30.0 + - - -
58G ILE* 6.0 7.0 - - + -
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Residues in contact with PRO 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TRP 5.3 0.8 - - - +
23G ARG 4.3 13.3 - - - +
24G GLU* 3.3 10.6 - - - +
25G GLU 3.2 0.8 - - - -
26G ARG* 1.3 76.9 - - - +
28G GLU* 1.3 58.1 + - - +
30G THR* 3.2 7.4 + - - -
31G LYS* 2.9 26.9 + - - +
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Residues in contact with GLU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLU 3.5 7.6 + - - +
25G GLU* 3.4 7.0 + - - +
27G PRO* 1.3 79.7 - - - +
29G VAL* 1.3 58.5 + - - +
31G LYS* 3.3 7.8 + - - +
32G LYS* 2.9 30.5 + - - +
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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
----------------------------------------------------------
25G GLU 2.9 19.2 + - - +
26G ARG* 3.5 9.4 - - - +
27G PRO 3.2 0.2 - - - -
28G GLU* 1.3 76.7 - - - +
30G THR* 1.3 57.7 + - - +
32G LYS* 3.3 7.2 + - - +
33G VAL* 2.9 28.3 + - - +
51G ASN* 5.1 4.0 - - - +
54G ARG* 5.8 9.0 - - + +
55G LEU* 5.8 8.7 - - + -
58G ILE* 6.0 5.4 - - + -
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Residues in contact with THR 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ARG 2.9 16.0 + - - -
27G PRO* 3.7 5.8 - - - -
29G VAL* 1.3 76.5 - - - +
31G LYS* 1.3 58.1 + - - +
33G VAL* 3.2 8.5 + - - +
34G THR* 2.9 29.8 + - - -
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Residues in contact with LYS 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G PRO 2.9 16.7 + - - +
28G GLU* 3.6 8.7 - - - +
29G VAL 3.2 0.2 - - - -
30G THR* 1.3 77.8 - - - +
32G LYS* 1.3 57.5 + - - +
34G THR* 3.3 6.5 + - - -
35G TRP* 2.9 28.6 + - - +
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Residues in contact with LYS 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G GLU 2.9 17.6 + - - +
29G VAL* 3.7 5.6 - - - +
31G LYS* 1.3 73.0 - - - +
33G VAL* 1.3 61.1 + - - +
35G TRP* 3.3 6.1 + - - +
36G ALA* 2.9 30.1 + - - +
51G ASN* 4.7 9.0 - - + +
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Residues in contact with VAL 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G VAL 2.9 14.4 + - - +
30G THR* 3.2 11.9 + - - +
32G LYS* 1.3 77.1 - - - +
34G THR* 1.3 56.3 + - - +
36G ALA* 3.3 4.8 + - - +
37G ALA* 2.9 27.8 + - - +
51G ASN* 4.2 20.5 - - + +
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Residues in contact with THR 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G THR 2.9 16.6 + - - -
31G LYS* 3.7 7.2 - - - -
33G VAL* 1.3 76.8 - - - +
35G TRP* 1.3 56.6 + - - +
37G ALA* 3.0 11.5 + - - +
38G SER* 2.9 25.8 + - - -
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Residues in contact with TRP 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G LYS 2.9 17.4 + - - +
32G LYS* 3.8 7.6 - - - +
34G THR* 1.3 76.5 - - - +
36G ALA* 1.3 61.8 + - - +
38G SER* 3.1 24.8 - - - +
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Residues in contact with ALA 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LYS 2.9 16.7 + - - +
33G VAL* 3.6 6.5 - - - +
35G TRP* 1.3 73.4 - - - +
37G ALA* 1.3 60.7 + - - +
38G SER 3.0 6.6 + - - +
40G GLY* 3.5 21.3 + - - -
41G ASP 4.0 1.4 + - - -
45G ASN* 5.7 1.1 - - + -
47G ASP* 4.4 11.9 - - + -
48G TYR* 3.9 39.3 - - + +
51G ASN* 5.2 0.4 - - + -
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Residues in contact with ALA 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C GLU* 5.6 6.3 - - - +
377C THR* 5.6 0.3 + - - -
380C ALA* 5.2 2.1 - - - +
33G VAL 2.9 14.3 + - - +
34G THR* 3.3 14.4 - - - +
36G ALA* 1.3 75.7 - - - +
38G SER* 1.3 56.8 + - - +
39G LEU 2.8 9.9 + - - -
40G GLY 3.8 2.8 + - - -
41G ASP* 4.4 17.0 + - + +
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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
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377C THR* 4.5 9.0 - - - -
34G THR 2.9 9.8 + - - -
35G TRP* 3.1 20.8 - - - +
36G ALA 3.0 4.4 - - - +
37G ALA* 1.3 71.8 - - - +
39G LEU* 1.3 65.4 + - - +
40G GLY 3.0 8.9 + - - -
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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