Contacts of the strand formed by residues 35 - 40 (chain G) in PDB entry 6KTR
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 VAL 35 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G CYS* 5.1 2.0 - - - -
29G VAL* 4.0 41.5 - - + +
32G TYR 5.1 0.7 - - - +
33G ASN 3.6 3.0 + - - -
34G TYR* 1.3 78.9 - - - +
36G SER* 1.3 64.7 + - - +
37G TRP* 3.9 18.4 - - + +
50G ILE* 4.2 1.6 - - - +
51G TYR* 3.7 1.6 - - - -
52G ASP 3.3 5.2 + - - -
53G VAL* 2.8 48.8 + - + +
68G LYS* 4.8 1.8 - - + -
73G ALA* 3.7 23.6 - - + -
90G CYS* 4.8 5.2 - - + -
91G SER 3.2 10.5 - - - +
92G SER* 4.6 3.1 - - - +
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Residues in contact with SER 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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104F LEU 5.4 0.2 + - - -
105F LEU* 3.5 23.1 - - - +
34G TYR 4.3 0.9 + - - -
35G VAL* 1.3 75.7 + - - +
37G TRP* 1.3 64.7 + - - +
38G TYR* 4.0 13.9 - - - -
48G LEU* 4.3 0.9 - - - -
50G ILE 3.1 11.8 + - - -
51G TYR* 4.3 2.8 - - - -
52G ASP 4.7 1.0 + - - -
89G TYR 4.5 0.2 - - - -
90G CYS* 3.2 5.9 - - - +
91G SER* 2.7 47.3 + - - +
302G NA 2.7 17.3 - - - -
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Residues in contact with TRP 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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6G GLN* 3.9 9.0 - - - -
20G ILE* 3.2 42.6 - - + -
21G SER 3.9 0.2 - - - -
22G CYS* 3.5 30.7 - - + -
35G VAL* 3.9 15.2 - - + +
36G SER* 1.3 77.9 - - - +
38G TYR* 1.3 61.6 + - - +
48G LEU* 3.8 4.3 - - - +
49G MET* 3.0 26.4 + - + -
50G ILE* 2.8 40.8 + - + +
53G VAL 4.8 3.9 + - - -
66G GLY* 5.1 0.7 - - - -
67G SER 5.3 0.2 + - - -
73G ALA* 4.1 2.9 - - + +
74G SER* 3.7 15.1 + - - -
75G LEU* 3.4 52.5 - - + +
88G TYR* 4.8 4.0 - - + -
89G TYR 3.3 9.9 - - - -
90G CYS* 3.6 25.6 - - + -
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Residues in contact with TYR 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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45F LEU* 5.0 1.3 - - + -
104F LEU 4.5 1.4 + - - -
105F LEU* 3.8 11.6 - - - +
106F PHE* 3.1 37.8 + + - +
109F TRP* 3.6 28.5 - + - -
36G SER* 4.0 7.6 - - - -
37G TRP* 1.3 77.8 - - - +
39G GLN* 1.3 59.5 + - - +
46G PRO* 4.1 15.7 - - + -
47G LYS 3.2 5.8 - - - +
48G LEU* 3.6 40.2 - - + -
49G MET* 4.5 1.1 - - - -
87G ASP 3.8 0.3 - - - +
88G TYR* 3.2 9.2 - - - +
89G TYR* 2.7 48.1 + - + +
91G SER* 3.7 21.8 - - - -
99G LEU* 5.2 0.9 - - + -
101G PHE* 4.1 23.6 - + - -
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Residues in contact with GLN 39 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G TYR* 1.3 73.7 - - - +
40G GLN* 1.3 61.1 + - - +
41G HIS* 3.6 30.8 + - + +
45G ALA 4.2 0.9 - - - +
46G PRO* 3.5 0.6 - - - +
47G LYS* 2.7 53.2 + - + +
49G MET* 3.6 36.3 - - + +
64G PHE* 4.4 4.9 - - - -
84G ASP* 4.4 7.5 + - - +
86G ALA* 4.0 14.4 - - + -
87G ASP 3.4 4.5 - - - -
88G TYR* 2.9 39.4 + - + -
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Residues in contact with GLN 40 (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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39F GLN* 2.7 43.4 + - - -
45F LEU* 4.3 1.3 - - - +
95F TYR* 3.6 10.5 + - - -
38G TYR 4.2 0.2 - - - -
39G GLN* 1.3 74.2 - - - +
41G HIS* 1.3 65.2 + - - +
42G PRO* 4.1 0.7 - - - +
43G GLY 6.2 0.2 - - - -
44G LYS 3.2 28.1 + - - +
45G ALA 4.5 0.9 - - - -
46G PRO* 3.9 28.1 - - + +
86G ALA* 3.3 3.3 - - - +
87G ASP* 2.8 49.7 + - + +
89G TYR* 3.5 17.0 + - + -
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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