Contacts of the strand formed by residues 32 - 39 (chain G) in PDB entry 5DK3
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 TYR 32 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27G TYR* 3.7 28.3 - + + +
28G THR* 3.8 9.0 - - - -
29G PHE 3.4 3.7 + - - +
30G THR 3.3 1.0 - - - -
31G ASN* 1.4 93.6 - - + +
33G TYR* 1.3 67.4 + - - +
52G ASN* 5.8 0.2 - - - -
53G PRO* 3.0 27.5 - - - +
98G ARG* 3.2 58.0 + - + -
99G ARG 3.3 5.6 - - - +
100G ASP* 3.4 46.7 + - + -
101G TYR* 4.0 4.0 - - - +
108G ASP* 4.5 5.6 + - - -
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Residues in contact with TYR 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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32G TYR* 1.3 77.0 - - - +
34G MET* 1.3 61.1 + - - +
35G TYR* 4.1 27.6 - + + -
50G GLY 5.4 0.9 - - - -
51G ILE 3.5 19.7 - - - +
52G ASN* 3.9 18.6 - - + +
53G PRO* 4.2 1.8 - - - -
57G GLY 5.2 2.5 - - - -
59G ASN* 5.4 12.6 + - - -
98G ARG* 3.2 8.7 - - - +
99G ARG* 2.7 79.9 + - - +
101G TYR* 3.1 44.4 + + - +
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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* 3.9 19.5 - - + -
22G CYS* 4.1 9.4 - - - +
24G ALA* 4.4 1.6 - - + -
27G TYR* 3.5 23.6 - - - +
29G PHE* 4.1 19.5 - - + -
32G TYR 4.0 0.2 + - - -
33G TYR* 1.3 73.4 - - - +
35G TYR* 1.3 67.8 + - - +
36G TRP* 4.2 6.7 - - - +
50G GLY* 3.4 1.2 - - - -
51G ILE* 2.9 47.7 + - + +
53G PRO* 4.6 6.7 - - + +
72G THR* 5.7 0.2 - - - +
79G ALA* 3.8 22.2 - - + -
96G CYS* 4.1 8.7 - - + -
97G ALA 3.6 28.0 - - - +
98G ARG* 3.9 4.9 - - + -
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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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98F LEU* 5.2 5.5 - - + +
100F LEU* 4.2 10.2 - - + +
33G TYR* 4.1 21.4 - + + -
34G MET* 1.3 74.1 - - - +
36G TRP* 1.4 65.1 + - - +
37G VAL* 4.3 2.7 - - + -
47G TRP* 3.2 36.3 - + + +
49G GLY 3.4 1.8 - - - +
50G GLY* 3.3 23.3 - - - -
59G ASN* 5.4 7.3 + - + -
96G CYS* 3.2 7.8 - - - +
97G ALA* 2.8 36.3 + - + +
99G ARG* 3.1 57.5 + - + -
107G PHE* 3.2 36.8 - + + -
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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 GLN* 4.2 7.9 - - - -
20G VAL* 3.9 32.5 - - + -
21G SER 4.4 0.2 - - - -
22G CYS* 3.7 24.9 - - + -
34G MET* 4.2 13.3 + - - +
35G TYR* 1.4 76.3 + - - +
37G VAL* 1.3 59.7 - - - +
47G TRP* 3.8 1.4 - - - -
48G MET* 2.8 45.4 + - + +
49G GLY 2.9 12.5 + - - +
51G ILE* 5.1 3.4 - - - +
70G LEU* 3.4 32.5 - - + +
71G THR 5.8 0.2 + - - -
79G ALA* 3.9 23.5 - - + +
80G TYR 3.9 7.1 + - - -
81G MET* 3.5 42.0 - - + -
94G TYR* 5.0 5.2 - + + -
95G TYR 3.3 18.4 - - - -
96G CYS* 3.8 12.8 - - + -
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Residues in contact with VAL 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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102F PHE* 4.1 6.3 - - + -
35G TYR* 5.0 2.0 - - + -
36G TRP* 1.3 81.1 - - - +
38G ARG* 1.3 62.5 + - - +
45G LEU* 4.0 30.5 - - + -
46G GLU 3.4 13.5 - - - +
47G TRP* 4.3 11.0 - - + -
48G MET* 4.5 2.9 - - - +
94G TYR* 3.6 1.6 - - - +
95G TYR* 2.7 42.8 + - + +
97G ALA* 5.4 2.5 - - + -
107G PHE* 4.0 28.0 - - + -
110G TRP* 4.0 28.3 - - + -
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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 VAL* 1.3 76.8 - - - +
39G GLN* 1.3 61.8 + - - +
40G ALA* 5.3 2.7 - - - +
44G GLY 3.9 0.7 - - - +
45G LEU* 3.6 4.0 - - - -
46G GLU* 2.8 62.9 + - + +
48G MET* 4.1 9.8 - - + +
64G PHE* 3.4 30.1 - - - -
83G LEU* 4.3 1.8 - - - +
89G ASP* 3.9 20.8 + - - -
90G ASP* 2.7 32.5 + - - +
92G ALA* 4.2 8.9 - - + +
93G VAL 3.3 11.4 - - - +
94G TYR* 3.0 44.3 + - + -
95G TYR* 5.1 0.7 - - - -
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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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42F GLN* 2.7 44.1 + - - -
91F TYR* 3.4 10.9 + - - -
38G ARG* 1.3 75.1 - - - +
40G ALA* 1.3 66.6 + - - +
41G PRO* 3.9 0.7 - - - +
42G GLY 5.8 0.2 - - - +
43G GLN 2.9 29.1 + - - +
44G GLY 3.7 6.9 - - - +
45G LEU* 3.7 19.2 - - + +
92G ALA* 3.4 3.7 - - - -
93G VAL* 2.9 38.6 + - + +
95G TYR* 4.1 12.2 + - + -
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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