Contacts of the strand formed by residues 29 - 37 (chain G) in PDB entry 4X6D
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 PHE 29 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2G GLU 4.3 8.3 - - - -
3G VAL* 4.0 8.3 - - + -
24G TYR* 3.5 27.7 + + + -
26G ASN* 3.5 34.5 - - + +
27G SER 3.1 7.8 - - - +
28G ALA* 1.3 78.5 - - - +
30G GLN* 1.3 65.4 + - - +
32G PHE* 3.6 21.4 - - + -
66G LYS* 4.2 5.9 - - - +
90G MET* 3.5 46.2 - - + -
91G SER 3.6 11.2 - - - +
92G THR* 3.5 24.7 - - + -
101G THR* 4.2 21.1 - - - -
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Residues in contact with GLN 30 (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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159A HIS* 4.6 7.3 - - - -
160A ASN* 4.2 14.3 - - - +
163A SER* 5.7 0.6 + - - -
164A ASP* 5.7 2.1 - - - +
27G SER 5.6 0.2 - - - +
28G ALA 4.0 1.0 - - - +
29G PHE* 1.3 75.2 - - - +
31G TYR* 1.3 72.9 + - + +
32G PHE* 3.4 9.5 - - - -
50G TYR* 3.2 40.2 + - + +
51G SER* 2.8 46.2 + - - -
66G LYS* 2.9 33.2 + - - +
91G SER 2.9 6.0 + - - +
93G SER* 3.8 18.4 + - - +
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Residues in contact with TYR 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASP* 5.5 0.2 - - + -
157A ILE* 4.0 16.0 - - + +
160A ASN* 2.7 36.2 + - - +
30G GLN* 1.3 83.5 - - + +
32G PHE* 1.3 63.9 + - - +
33G MET* 4.0 13.0 - - - +
48G TYR* 3.7 25.6 - + + -
49G THR 3.9 2.0 - - - -
50G TYR* 3.3 27.1 - + - -
90G MET* 3.1 8.7 - - - +
91G SER* 3.0 43.6 + - - -
92G THR 3.7 23.3 - - - -
93G SER* 4.4 0.2 - - - -
94G LEU* 3.6 18.3 - - + +
96G ASN* 4.0 10.8 - - - -
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Residues in contact with PHE 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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24G TYR* 3.8 32.5 - + - -
29G PHE* 3.6 31.9 - - + -
30G GLN* 3.4 24.9 - - - -
31G TYR* 1.3 73.6 - - - +
33G MET* 1.3 62.6 + - - +
34G TRP* 5.5 3.8 - - + -
47G MET 4.1 0.3 - - - +
48G TYR* 3.3 4.9 - - - -
49G THR* 2.9 42.5 + - - +
51G SER* 4.1 10.8 - - - -
64G VAL* 3.6 40.8 - - + -
66G LYS* 4.5 3.4 - - + -
71G ILE* 3.8 21.3 - - + -
89G ALA 3.6 2.7 - - - +
90G MET* 3.7 18.8 - - + -
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Residues in contact with MET 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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31G TYR* 4.0 11.0 - - - +
32G PHE* 1.3 85.0 - - - +
34G TRP* 1.3 63.4 + - - +
35G TYR* 3.9 25.6 - - + +
45G LEU* 3.9 18.8 - - + -
47G MET 3.5 2.9 - - - -
48G TYR* 3.9 22.4 - - + -
71G ILE* 5.2 1.3 - - - +
88G CYS* 3.3 6.2 - - - +
89G ALA* 2.7 59.0 + - + +
90G MET 4.0 1.3 - - - +
91G SER* 3.9 21.5 - - - +
100G SER* 3.9 13.5 - - - -
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Residues in contact with TRP 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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5G GLN* 3.7 21.1 - - - -
20G LEU* 3.6 33.2 - - + -
21G ASN 4.1 0.7 - - - -
22G CYS* 3.8 16.8 - - - -
32G PHE* 5.5 3.1 - - + -
33G MET* 1.3 75.1 - - - +
35G TYR* 1.3 63.1 + - - +
45G LEU* 3.5 3.0 - - - +
46G LEU* 2.8 26.3 + - + +
47G MET* 2.7 28.0 + - + +
62G ALA* 4.4 18.8 - - + +
63G GLN 5.3 0.8 + - - +
71G ILE* 4.0 21.6 - - + +
72G SER* 3.9 11.3 + - - +
73G LEU* 3.5 52.4 - - + +
86G TYR* 4.3 10.3 - - + -
87G LEU 3.5 17.0 - - - -
88G CYS* 3.8 13.5 - - + -
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Residues in contact with TYR 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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33G MET* 3.9 24.0 - - + +
34G TRP* 1.3 75.8 - - - +
36G ARG* 1.3 59.9 + - - +
43G PRO* 4.2 22.0 - - + -
44G GLU* 3.4 8.1 - - - +
45G LEU* 3.3 47.3 - - + +
46G LEU* 4.4 1.8 - - - -
86G TYR* 3.2 8.5 - - - +
87G LEU* 2.6 53.0 + - + +
89G ALA* 4.0 7.6 - - + -
100G SER* 5.3 2.8 + - - -
102G PHE* 3.5 35.6 - + + -
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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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35G TYR* 1.3 74.6 - - - +
37G GLN* 1.3 63.6 + - - +
38G TYR* 3.0 47.9 + - + -
42G GLY 4.2 0.7 - - - +
43G PRO* 4.6 0.2 - - - -
44G GLU* 2.9 56.8 + - + +
46G LEU* 3.4 46.3 - - + +
60G PHE* 4.2 15.8 - - - -
81G SER 5.4 0.4 - - - -
82G ASP* 4.6 5.3 + - - -
84G ALA* 3.7 15.9 - - + -
85G THR 3.4 3.1 - - - -
86G TYR* 3.7 23.1 + - + -
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Residues in contact with GLN 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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36G ARG* 1.3 74.3 - - - +
38G TYR* 1.3 65.7 + - - +
39G SER 3.9 0.2 + - - -
41G LYS 2.8 28.9 + - - +
42G GLY* 4.0 6.9 - - - -
43G PRO* 3.7 26.4 - - + +
84G ALA* 4.1 1.8 - - - -
85G THR* 2.6 45.0 + - - +
87G LEU* 3.9 26.3 - - + +
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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