Contacts of the strand formed by residues 61 - 66 (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 PHE 61 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46Y TRP* 3.4 38.4 - + + -
53Y LEU* 3.3 23.6 - - + +
57Y VAL* 3.4 26.2 - - + -
58Y PRO* 3.0 19.7 + - + +
59Y SER 3.5 6.4 - - - +
60Y ARG* 1.3 82.4 - - + +
62Y SER* 1.3 61.9 + - - +
72Y LEU* 3.7 19.7 - - + -
73Y THR 3.4 1.3 - - - -
74Y ILE* 3.4 30.1 - - + -
81Y ASP* 3.4 33.4 - - + -
85Y TYR* 3.4 30.5 - + - -
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Residues in contact with SER 62 (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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47Y ILE* 3.8 4.9 - - - -
51Y SER 5.2 0.7 - - - -
53Y LEU* 4.2 5.8 - - - -
59Y SER 5.7 0.2 - - - -
60Y ARG 4.6 2.4 + - - -
61Y PHE* 1.3 79.1 - - - +
63Y GLY* 1.3 62.4 + - - +
72Y LEU* 3.4 2.6 - - - +
73Y THR* 2.7 55.1 + - - +
75Y SER* 5.7 1.0 + - - -
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Residues in contact with GLY 63 (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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34Y TRP* 5.1 0.9 - - - -
47Y ILE* 3.8 14.5 - - - +
50Y THR 3.3 20.0 - - - -
51Y SER* 3.2 25.9 + - - +
62Y SER* 1.3 77.1 - - - +
64Y SER* 1.3 64.4 + - - -
71Y THR 3.1 9.9 - - - -
72Y LEU* 4.4 0.2 - - - -
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Residues in contact with SER 64 (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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34Y TRP* 5.4 0.4 + - - +
50Y THR* 3.6 16.0 + - - -
51Y SER* 5.0 1.1 - - - -
63Y GLY* 1.3 77.0 - - - -
65Y GLY* 1.3 64.7 + - - +
70Y TYR* 3.3 5.4 - - - +
71Y THR* 2.6 50.4 + - - +
73Y THR* 6.0 0.7 - - - -
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Residues in contact with GLY 65 (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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50Y THR* 3.9 6.9 - - - +
64Y SER* 1.3 84.6 + - - +
66Y SER* 1.3 68.6 - - - -
69Y ASP 3.3 12.6 - - - -
70Y TYR* 3.3 14.5 - - - -
71Y THR* 5.9 0.9 - - - -
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Residues in contact with SER 66 (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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264B TYR* 4.9 4.5 - - - -
65Y GLY* 1.3 78.4 - - - -
67Y GLY* 1.3 68.4 + - - +
68Y THR 2.9 4.5 + - - -
69Y ASP* 3.1 18.4 + - - +
70Y TYR* 3.2 17.4 - - - -
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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