Contacts of the strand formed by residues 84 - 89 (chain Y) in PDB entry 1MHP
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 THR 84 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35Y TYR 4.0 0.3 - - - +
36Y GLN* 3.8 0.2 - - - -
37Y GLN* 3.0 51.6 + - + +
39Y PRO* 5.5 2.7 - - + -
83Y ALA* 1.3 76.3 - - - +
85Y TYR* 1.3 61.9 + - - +
86Y TYR* 4.0 23.2 + - + +
100Y GLY 4.4 1.4 - - - -
101Y THR 3.2 20.9 + - - -
102Y LYS* 3.9 29.0 + - + +
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Residues in contact with TYR 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y GLN* 2.8 28.0 + - - -
21Y ILE* 3.9 17.0 - - + -
34Y TRP* 4.6 3.4 - - + -
35Y TYR 3.3 7.0 - - - +
36Y GLN* 3.4 36.3 + - + -
46Y TRP* 3.9 8.3 - + - -
61Y PHE* 3.4 34.9 - + - -
72Y LEU* 3.5 26.5 - - + -
74Y ILE* 4.6 4.5 - - + -
81Y ASP 2.6 29.3 + - - -
83Y ALA 3.5 21.7 + - - -
84Y THR* 1.3 74.4 - - - +
86Y TYR* 1.3 56.4 + - - +
101Y THR 2.8 22.7 + - - -
103Y VAL* 3.9 18.8 - - + -
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Residues in contact with TYR 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X GLN* 3.0 23.5 + - - -
43X LYS 4.2 4.0 + - - -
44X GLY* 4.1 14.4 - - - -
45X LEU* 3.9 24.5 - - + -
6Y GLN* 3.1 4.9 - - - +
34Y TRP* 3.1 8.2 - - - -
35Y TYR* 2.7 46.5 + - + +
37Y GLN* 3.4 31.0 + - + -
84Y THR* 4.0 23.4 + - + +
85Y TYR* 1.3 77.1 - - - +
87Y CYS* 1.3 65.1 + - - +
97Y PHE* 4.5 12.6 - - + -
98Y GLY 3.6 11.9 - - - +
99Y GLN 3.6 19.0 + - - -
100Y GLY* 3.4 17.5 - - - -
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Residues in contact with CYS 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y LEU* 4.2 2.0 - - - -
6Y GLN* 2.7 29.7 + - - -
23Y CYS* 2.0 49.6 - - + -
32Y MET* 4.1 2.9 - - + -
33Y PHE 3.1 8.3 - - - +
34Y TRP* 3.5 22.4 - - + -
86Y TYR* 1.3 75.5 - - - +
88Y GLN* 1.3 60.5 + - - +
97Y PHE* 3.3 4.9 - - - +
98Y GLY* 2.9 31.5 + - - -
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Residues in contact with GLN 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X GLY 2.9 24.4 + - - +
105X PHE* 3.8 7.9 - - + -
4Y LEU* 3.8 1.8 - - - -
32Y MET* 3.2 7.2 - - - +
33Y PHE* 2.6 44.3 + - + +
35Y TYR* 2.7 44.7 + - + -
87Y CYS* 1.3 77.3 - - - +
89Y GLN* 1.3 87.8 + - - +
90Y TRP* 3.8 4.2 - - - +
95Y TRP* 4.4 8.5 - - + +
96Y THR 3.1 19.1 - - - +
97Y PHE* 3.8 20.9 - - + -
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Residues in contact with GLN 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y ILE* 3.5 20.2 - - + +
4Y LEU* 3.4 30.0 - - + +
29Y VAL* 4.5 9.6 - - + -
31Y HIS 4.9 4.3 - - - +
32Y MET* 4.1 12.6 - - + -
33Y PHE* 4.9 1.8 - - - -
88Y GLN* 1.3 92.1 + - - +
90Y TRP* 1.3 56.9 + - - +
91Y SER* 3.3 4.4 + - - +
92Y GLY 2.8 42.7 + - - -
94Y PRO 3.4 4.0 + - - -
95Y TRP* 3.5 2.3 - - - +
96Y THR* 3.0 46.1 + - - +
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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