Contacts of the strand formed by residues 33 - 39 (chain G) in PDB entry 6I53
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 ILE 33 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 4.9 11.4 - - + -
31G ALA 5.5 0.7 - - - +
32G TYR* 1.3 71.8 - - - +
34G MET* 1.3 61.6 + - - +
50G ALA* 4.0 9.9 - - + -
51G MET 3.7 15.0 - - - +
52G ASP* 3.3 30.5 - - - +
97G ALA* 3.4 0.2 - - - -
98G GLY 2.9 36.1 + - - +
99G ALA* 4.0 22.9 - - - +
100G GLY* 4.7 4.7 - - - -
104G LEU* 3.8 35.9 - - + -
110G TYR* 3.3 22.0 - - + +
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Residues in contact with MET 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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4G LEU* 4.7 5.8 - - + -
22G CYS 4.6 2.7 - - - +
24G ALA* 4.5 18.4 - - + -
29G PHE* 3.7 23.8 - - + +
32G TYR 3.8 1.5 + - - +
33G ILE* 1.3 74.4 - - - +
35G ALA* 1.3 59.1 + - - +
51G MET* 3.3 26.5 + - - +
69G ILE* 3.8 8.1 - - - +
71G ARG* 3.4 39.3 - - - +
76G ASN* 4.2 4.7 - - - +
77G SER* 4.0 18.8 - - - +
78G VAL* 3.8 33.4 - - + +
95G CYS* 4.7 7.9 - - - -
96G ALA 3.4 7.6 - - - +
97G ALA* 4.1 8.5 - - + -
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Residues in contact with ALA 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 ILE 3.8 0.6 + - - -
34G MET* 1.3 73.9 - - - +
36G TRP* 1.3 68.8 + - - +
37G PHE* 4.2 10.3 - - + -
47G PHE* 4.2 2.5 - - + -
49G ALA 3.3 13.9 - - - +
50G ALA* 3.7 7.4 - - + +
78G VAL* 5.3 0.3 - - - +
95G CYS* 3.7 5.9 - - - -
96G ALA* 2.9 30.8 + - - +
110G TYR* 3.4 37.0 - - + +
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Residues in contact with TRP 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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6G GLU* 4.8 3.6 - - + -
20G VAL* 3.6 44.9 - - + -
21G SER 3.6 13.7 - - - -
22G CYS* 3.6 12.3 - - + -
35G ALA* 1.3 75.9 - - - +
37G PHE* 1.3 72.0 + - - +
47G PHE* 3.9 2.8 - - - -
48G LEU* 3.3 25.3 + - + -
49G ALA* 2.8 14.5 + - + +
69G ILE* 3.6 22.2 - - + -
78G VAL* 3.6 32.4 - - + +
79G ASP 3.5 16.0 + - - -
80G LEU* 3.5 36.1 - - + +
93G TYR* 4.6 14.6 - - + -
94G TYR 3.2 29.8 - - - -
95G CYS* 4.0 10.3 - - + -
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Residues in contact with PHE 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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35G ALA* 4.2 4.7 - - + -
36G TRP* 1.3 83.5 - - - +
38G ARG* 1.3 60.6 + - - +
45G ARG* 4.7 9.6 - - + -
46G GLU 3.3 20.6 - - - -
47G PHE* 3.7 31.4 - + + -
48G LEU* 3.4 14.3 - - - +
93G TYR* 3.4 6.4 - - - +
94G TYR* 3.0 39.8 + - + +
96G ALA* 3.8 11.2 - - + -
105G ARG 4.3 5.8 - - - -
106G THR 4.6 0.9 - - - -
107G ALA* 4.0 26.7 - - + -
110G TYR* 3.5 40.8 - + - -
113G TRP* 3.6 25.1 - + + -
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Residues in contact with ARG 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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37G PHE* 1.3 79.9 - - - +
39G GLN* 1.3 61.7 + - - +
40G ALA* 4.0 3.0 + - + +
44G GLU 3.6 0.9 - - - +
45G ARG* 3.3 1.2 - - - -
46G GLU* 2.5 86.0 + - + +
48G LEU* 3.7 21.5 - - + +
62G SER* 3.9 3.2 + - - -
63G VAL* 3.8 23.0 - - - +
67G PHE* 4.8 1.6 - - - -
88G GLU 4.9 5.1 + - - -
89G ASP* 2.5 38.7 + - - +
91G ALA* 3.7 15.3 - - + -
92G VAL 3.6 6.1 - - - -
93G TYR* 3.6 26.0 + - + -
94G TYR* 5.2 0.4 - - - -
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Residues in contact with GLN 39 (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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38G ARG* 1.3 73.7 - - - +
40G ALA* 1.3 67.1 + - - +
41G PRO* 3.9 1.4 - - - +
43G LYS 3.4 20.5 + - - +
44G GLU* 3.9 8.6 - - - +
45G ARG* 3.9 24.7 + - + +
91G ALA* 3.4 11.9 - - - +
92G VAL* 3.1 20.7 + - + +
94G TYR* 3.3 38.7 + - + -
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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
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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