Contacts of the helix formed by residues 27 - 38 (chain G) in PDB entry 6R90
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 27 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G SER* 3.6 3.4 - - - +
25G GLN 3.7 0.6 - - - +
26G PHE* 1.3 90.4 - - + +
28G VAL* 1.3 66.0 + - - +
29G GLY 3.3 1.1 - - - +
30G ARG* 4.0 26.7 - - + +
31G VAL* 3.2 22.8 + - + +
53G ALA* 5.4 0.9 - - - -
38H TYR* 4.5 11.4 - - + -
41H TYR* 3.3 47.8 - - + +
121I G 3.9 9.6 - - - +
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Residues in contact with VAL 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 3.9 38.6 - - + +
19G SER* 2.6 42.1 + - - +
22G ALA* 5.4 2.9 - - + -
24G LEU* 5.9 3.4 - - + -
26G PHE 4.3 3.1 - - - +
27G PRO* 1.3 72.1 - - - +
29G GLY* 1.3 63.5 + - - +
31G VAL* 3.2 7.2 + - - +
32G HIS* 2.9 21.1 + - - +
49G PRO* 4.6 8.8 - - + +
50G VAL* 4.2 33.7 - - + -
53G ALA* 4.9 9.2 - - + -
30J A 5.5 0.4 - - - +
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Residues in contact with GLY 29 (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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18G ARG* 5.1 2.7 - - - -
19G SER* 4.4 0.6 + - - -
27G PRO* 3.3 1.2 - - - +
28G VAL* 1.3 81.5 - - - +
30G ARG* 1.3 62.1 + - - +
32G HIS* 3.3 6.9 + - - +
33G ARG* 3.0 21.1 + - - +
29J A 3.3 37.4 + - - +
30J A 4.6 7.1 + - - -
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Residues in contact with ARG 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PRO* 3.7 27.2 + - + +
28G VAL 3.3 0.4 - - - -
29G GLY* 1.3 75.7 - - - +
31G VAL* 1.3 58.7 + - - +
33G ARG* 3.4 9.5 + - - +
34G LEU* 2.9 50.6 + - + +
36H GLU* 2.6 43.9 + - - +
37H SER 2.9 19.0 + - - +
38H TYR* 4.8 11.9 - - + +
41H TYR* 4.6 5.4 + - - -
121I G 2.5 37.6 + - - -
122I T 2.5 25.2 + - - -
28J A 5.9 4.2 - - - -
29J A 3.3 14.6 + - - +
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Residues in contact with VAL 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 5.9 2.0 - - + -
27G PRO* 3.2 18.1 + - + +
28G VAL* 3.2 9.5 + - - +
30G ARG* 1.3 77.8 - - - +
32G HIS* 1.3 64.5 + - - +
34G LEU* 3.2 8.0 + - - +
35G LEU* 2.9 26.9 + - + +
49G PRO* 3.7 31.2 - - + +
52G LEU* 4.6 6.5 - - + -
53G ALA* 4.8 13.0 - - + +
56G LEU* 5.2 5.6 - - + -
38H TYR* 4.7 18.2 - - + +
71H PHE* 3.9 24.4 - - + -
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Residues in contact with HIS 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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18G ARG* 3.3 36.8 + - - +
28G VAL 2.9 16.1 + - - +
29G GLY* 3.6 7.2 - - - +
31G VAL* 1.3 78.2 - - - +
33G ARG* 1.3 57.0 + - - +
35G LEU* 3.2 3.9 + - - +
36G ARG* 2.9 63.1 + - + +
44G VAL* 4.3 30.3 + - + +
45G GLY 5.4 0.2 + - - -
46G ALA* 5.6 3.1 - - + -
49G PRO* 4.2 17.0 - - + +
112I A 5.4 7.0 + - - -
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Residues in contact with ARG 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 GLY 3.0 16.8 + - - +
30G ARG* 3.9 11.9 - - - +
32G HIS* 1.3 76.9 - - - +
34G LEU* 1.3 78.7 + - - +
36G ARG* 3.2 25.5 + - + +
37G LYS* 3.0 33.2 + - + +
36H GLU* 2.8 44.2 + - - -
28J A 3.6 28.1 + - - -
29J A 3.2 34.3 + - - +
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Residues in contact with LEU 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 ARG* 2.9 40.3 + - + +
31G VAL* 3.6 7.0 - - - +
33G ARG* 1.3 92.9 - - - +
35G LEU* 1.3 59.8 + - - +
37G LYS* 3.5 4.3 + - + +
38G GLY* 2.8 28.6 + - - -
40G TYR* 4.4 1.9 - - - -
36H GLU* 5.4 2.2 - - - +
38H TYR* 3.2 28.3 - - + +
68H ASN* 5.6 3.1 - - - +
71H PHE* 3.8 21.2 - - + -
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Residues in contact with LEU 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 VAL* 2.9 34.2 + - + +
32G HIS* 3.2 4.7 + - - +
34G LEU* 1.3 75.7 - - - +
36G ARG* 1.3 64.6 + - - +
38G GLY* 3.3 7.4 + - - -
39G ASN 4.2 2.3 + - - -
40G TYR* 3.8 37.0 + - + +
41G SER 5.1 3.1 - - - +
44G VAL* 4.0 40.5 - - + +
48G ALA* 5.3 1.8 - - + -
49G PRO* 4.3 13.5 - - + -
52G LEU* 4.5 10.8 - - + -
71H PHE* 3.8 15.0 - - + -
75H ALA* 3.9 17.7 - - + -
90H ILE* 5.8 5.4 - - + -
95H ILE* 5.6 6.1 - - + -
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Residues in contact with ARG 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 HIS* 2.9 66.7 + - + +
33G ARG* 3.2 21.8 + - + +
35G LEU* 1.3 77.5 - - - +
37G LYS* 1.3 59.1 + - - +
39G ASN* 4.3 6.6 + - - -
41G SER 5.2 6.1 - - - +
44G VAL* 5.2 8.7 - - + +
112I A 5.6 6.5 - - - -
29J A 5.9 0.6 + - - -
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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
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83D HIS* 4.9 13.4 + - + +
86D LYS* 3.3 34.0 - - - +
33G ARG* 3.0 24.2 + - + +
34G LEU* 4.3 3.8 - - + +
36G ARG* 1.3 73.3 - - + +
38G GLY* 1.3 58.8 + - - +
39G ASN* 3.1 23.6 + - - +
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Residues in contact with GLY 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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83D HIS* 5.4 12.2 - - - -
34G LEU 2.8 18.4 + - - -
35G LEU 3.3 2.8 + - - -
37G LYS* 1.3 75.0 - - - +
39G ASN* 1.3 71.0 + - - +
40G TYR* 3.3 32.0 + - - -
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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