Contacts of the strand formed by residues 60 - 66 (chain A) in PDB entry 4HK4
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.1 1.8 - - + -
20A LEU* 4.3 5.4 - - + -
23A VAL* 3.8 15.5 - - + -
24A LEU* 3.6 29.6 - - + -
29A LYS* 3.4 32.5 - - + -
30A SER 3.6 20.9 - - - -
31A ALA* 3.9 4.9 - - + -
55A LEU* 3.1 49.3 + - + +
56A GLN* 3.4 22.1 + - - +
58A ALA* 4.1 5.8 - - + -
59A GLY* 1.3 78.1 - - - +
61A ASP* 1.3 61.8 + - - +
62A ILE* 3.6 13.1 + - + +
166A VAL* 3.7 27.4 - - + -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 4.9 10.7 - - - +
29A LYS 2.9 28.6 + - - +
30A SER* 3.2 11.5 - - - -
31A ALA 2.8 24.9 + - - +
59A GLY 4.5 3.8 - - - +
60A PHE* 1.3 72.3 - - - +
62A ILE* 1.3 60.9 + - - +
63A ILE* 3.9 4.8 - - + +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.3 21.8 - - + -
52A MET* 3.6 38.4 - - + +
55A LEU* 4.0 2.0 - - + -
56A GLN* 3.7 33.2 - - + +
60A PHE* 3.7 10.8 - - + +
61A ASP* 1.3 81.1 - - - +
63A ILE* 1.3 67.5 + - - +
64A ILE* 4.2 10.1 - - + -
98A LEU* 4.2 11.9 - - + -
99A LYS 4.3 3.7 + - - +
100A ALA* 3.1 24.3 - - + +
101A LYS* 2.9 24.6 + - - +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER* 4.0 9.0 - - - -
31A ALA 2.9 8.1 + - - +
32A GLU* 3.1 26.1 - - + +
33A ILE 3.2 5.2 + - - -
61A ASP* 3.9 14.4 - - + +
62A ILE* 1.3 81.3 - - - +
64A ILE* 1.3 68.0 + - - +
65A SER 4.4 1.1 - - - +
101A LYS* 3.4 29.8 - - + +
103A VAL* 3.8 33.4 - - + -
162A VAL* 3.9 25.6 - - + +
164A VAL* 3.9 22.9 - - + -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.4 26.5 - - + +
35A PHE* 4.0 21.3 - - + -
49A ILE* 4.2 9.4 - - + -
52A MET* 4.6 1.3 - - + -
62A ILE* 4.2 7.4 - - + -
63A ILE* 1.3 76.2 - - - +
65A SER* 1.3 61.8 + - - +
66A LEU* 3.5 12.1 + - + -
93A PHE* 4.1 11.4 - - + -
98A LEU* 3.9 26.2 - - + -
100A ALA* 4.3 3.6 - - + -
101A LYS 2.7 10.7 + - - +
102A TYR* 3.4 38.7 - - + +
103A VAL 3.1 22.9 + - - -
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.7 15.5 - - - -
33A ILE 2.8 16.1 + - - +
34A GLY* 3.2 6.0 - - - -
35A PHE 2.9 27.2 + - - -
63A ILE* 3.7 2.4 + - - -
64A ILE* 1.3 73.5 - - - +
66A LEU* 1.3 61.8 + - - +
67A ALA* 3.3 6.8 + - - +
103A VAL* 3.4 20.1 + - - +
105A GLY* 5.0 4.3 + - - -
108A PHE* 5.0 2.4 - - - -
158A ASN* 4.9 17.2 + - - +
162A VAL* 5.0 6.3 - - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.7 10.3 - - + +
37A PRO* 4.6 7.2 - - + -
64A ILE* 4.1 24.5 - - + +
65A SER* 1.3 68.9 - - - +
67A ALA* 1.3 52.8 + - - +
68A ASP* 2.7 28.6 + - - +
86A GLY* 3.9 15.5 - - - +
89A ASN* 4.7 7.0 - - + -
90A LYS* 4.4 7.2 - - + +
93A PHE* 4.2 17.9 - - + -
102A TYR* 4.2 21.8 - - + -
103A VAL 3.0 9.3 + - - +
104A TYR* 3.5 48.7 - - + +
105A GLY 3.2 10.8 + - - -
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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