Contacts of the strand formed by residues 57 - 65 (chain P) in PDB entry 1HH2
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 LYS 57 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P ILE* 4.6 13.2 - - + -
46P GLU 3.9 0.3 - - - +
47P VAL* 3.7 1.4 - - - -
48P VAL* 3.1 36.3 + - + +
55P ASN* 3.1 12.2 + - + +
56P ILE* 1.3 77.0 - - - +
58P VAL* 1.3 63.8 + - - +
59P TYR* 3.0 30.6 + - + +
96P GLU* 3.0 40.2 + - + +
97P LEU 4.8 3.4 - - - +
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Residues in contact with VAL 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P MET* 4.6 17.0 - - - +
35P TYR* 4.0 29.4 - - + -
45P VAL* 4.4 8.1 - - + -
46P GLU 3.2 10.1 - - - +
47P VAL* 4.2 15.5 - - + -
56P ILE* 4.7 4.3 - - + +
57P LYS* 1.3 80.8 - - - +
59P TYR* 1.3 64.3 + - - +
96P GLU* 3.5 7.1 - - - +
97P LEU* 2.9 62.1 + - + -
98P ASN 4.9 6.8 + - - +
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Residues in contact with TYR 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P VAL* 3.2 7.8 - - - -
46P GLU* 2.9 38.7 + - + +
48P VAL* 3.5 38.1 - - + -
57P LYS* 3.0 38.3 + - + -
58P VAL* 1.3 76.3 - - - +
60P GLN* 1.3 60.0 + - - +
61P LEU* 3.4 3.4 - - + +
94P LYS* 3.8 32.3 - - + -
95P LYS 3.2 5.8 - - - +
96P GLU* 3.1 47.0 + - + -
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Residues in contact with GLN 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P LYS* 3.5 39.4 - - + +
44P ASN 3.5 10.8 - - - +
45P VAL* 4.3 3.8 - - + -
59P TYR* 1.3 73.1 - - - +
61P LEU* 1.3 70.3 + - - +
62P LEU* 3.7 14.2 + - + +
71P PRO 4.6 0.3 - - - +
72P ALA* 2.7 29.8 - - - +
93P VAL 3.6 0.9 - - - +
94P LYS* 3.6 1.4 - - - -
95P LYS* 2.7 42.7 + - + +
97P LEU* 3.6 28.8 - - + +
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Residues in contact with LEU 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ASN* 2.9 46.3 + - + +
45P VAL 3.5 3.8 - - - +
46P GLU* 3.5 34.8 - - + +
59P TYR* 3.4 18.8 - - + +
60P GLN* 1.3 76.7 - - - +
62P LEU* 1.3 67.8 + - - +
72P ALA 4.4 3.1 - - - +
73P THR* 4.6 5.0 - - - +
92P ILE* 4.0 19.5 - - + -
93P VAL 3.5 4.9 - - - -
94P LYS* 4.6 10.1 - - + +
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Residues in contact with LEU 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P GLN* 3.9 15.0 - - + +
61P LEU* 1.3 79.9 - - - +
63P GLU* 1.3 63.3 + - - +
64P VAL 3.6 0.3 + - - -
71P PRO 4.1 4.9 - - - +
72P ALA 3.4 27.1 - - - +
73P THR* 3.6 16.8 - - - +
74P GLN 4.1 3.6 - - - +
75P ILE* 3.7 39.8 - - + +
83P ILE* 5.1 1.3 - - + -
92P ILE* 3.4 6.1 - - - +
93P VAL* 2.8 39.4 + - + +
95P LYS* 4.2 31.6 - - + +
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Residues in contact with GLU 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62P LEU* 1.3 71.6 - - - +
64P VAL* 1.3 67.2 + - - +
65P VAL* 3.4 22.4 + - + +
73P THR* 5.2 1.7 - - - +
74P GLN* 3.0 25.0 + - + +
75P ILE 2.8 22.8 + - - -
90P GLY* 5.3 8.2 - - - -
91P SER 3.7 5.4 - - - +
92P ILE* 3.8 18.8 - - + +
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Residues in contact with VAL 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62P LEU 4.4 1.1 - - - +
63P GLU* 1.3 72.9 - - - +
65P VAL* 1.3 65.7 + - - +
75P ILE* 3.3 8.1 - - + +
77P LEU* 3.7 33.4 - - + +
80P ALA* 3.6 24.2 - - + -
87P ALA* 4.4 1.1 - - + -
88P GLU 3.5 24.0 - - - +
89P VAL* 3.6 9.6 - - + +
90P GLY* 3.0 25.1 + - - -
91P SER* 2.9 26.8 + - - +
93P VAL* 3.8 15.5 - - + -
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Residues in contact with VAL 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P GLU* 3.8 30.1 - - - +
64P VAL* 1.3 80.2 - - - +
66P GLU* 1.3 61.6 + - - +
67P GLU 3.5 27.1 - - - +
68P VAL* 4.0 3.8 - - + -
74P GLN* 3.7 34.1 - - + +
75P ILE 2.8 17.6 + - - +
76P SER* 3.9 11.4 - - - -
77P LEU* 4.0 5.7 + - - +
89P VAL* 4.2 12.6 - - - +
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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