Contacts of the strand formed by residues 64 - 68 (chain A) in PDB entry 4MNY
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 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.1 8.5 - - + -
34A TYR 3.3 14.1 - - - -
35A ARG* 3.8 22.0 - - + -
36A ARG* 5.1 0.7 + - - -
41A VAL* 4.0 12.6 - - + -
58A CYS 4.3 2.1 + - - -
59A PHE* 3.5 45.3 - + - -
60A TYR* 2.5 41.7 + - - +
61A LYS 3.2 25.1 - - - -
62A LYS* 3.1 23.9 + - - +
63A ASP* 1.3 80.3 - - + +
65A ILE* 1.3 65.3 + - - +
83A PHE 4.3 4.7 - - - +
84A GLU* 4.5 4.2 - - - +
85A VAL* 3.8 26.0 + - + +
88A LEU* 4.2 9.9 - - + -
106A LEU* 5.2 1.1 - - + -
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA 3.7 1.2 - - - +
33A ILE* 3.5 3.1 - - - +
34A TYR* 2.8 44.6 + - + +
36A ARG* 3.4 41.7 - - + +
38A VAL* 3.9 31.0 - - + -
63A ASP 4.4 2.2 - - - +
64A TYR* 1.3 79.7 - - - +
66A VAL* 1.3 63.5 + - - +
67A TYR* 3.6 27.8 - - + +
82A LYS* 3.7 28.9 - - + +
83A PHE 3.7 4.5 - - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 4.1 18.6 - - + -
32A ALA 3.5 4.3 - - - +
33A ILE* 4.3 10.1 - - + -
52A VAL* 4.3 6.1 - - + -
65A ILE* 1.3 76.8 - - - +
67A TYR* 1.3 75.3 + - - +
68A LEU* 4.4 5.8 - - + -
82A LYS* 3.5 3.6 - - - +
83A PHE* 2.7 44.3 + - + +
85A VAL* 3.8 26.0 - - + -
106A LEU* 4.1 17.0 - - + -
108A ILE* 4.1 24.0 - - + -
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Residues in contact with TYR 67 (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 PHE 4.2 0.3 - - - +
31A ALA* 3.3 7.4 - - - +
32A ALA* 2.9 36.5 + - + +
34A TYR* 3.5 30.3 - + - -
65A ILE* 3.6 19.7 - - + +
66A VAL* 1.3 76.7 - - - +
68A LEU* 1.3 62.2 + - - +
70A ARG* 3.5 51.9 + - + +
76A ASN* 5.6 0.5 + - - -
80A GLU* 3.8 17.3 - - + -
81A MET 3.4 12.6 - - - -
82A LYS* 3.7 35.1 + - + +
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Residues in contact with LEU 68 (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 PRO 5.6 2.5 - - - +
29A TRP 4.9 0.7 - - - +
30A PHE 4.3 6.3 - - - +
31A ALA* 3.5 33.0 - - + +
46A LEU* 4.0 17.0 - - + -
52A VAL* 4.5 7.6 - - + -
66A VAL* 4.4 5.4 - - + -
67A TYR* 1.3 75.6 - - - +
69A GLY* 1.3 65.7 + - - +
70A ARG* 3.3 3.7 + - - +
80A GLU* 3.2 2.9 - - - +
81A MET 2.9 32.1 + - - +
83A PHE* 3.5 26.2 - - + -
108A ILE* 3.9 9.6 - - + -
112A ALA* 3.6 24.7 - - + -
118A ILE* 3.9 26.5 - - + -
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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