Contacts of the strand formed by residues 72 - 75 (chain A) in PDB entry 3K4H
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 GLY 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR 3.9 3.4 + - - -
11A LEU* 3.4 4.5 - - - +
12A GLY 2.8 22.0 + - - -
70A ILE* 3.1 8.5 - - - +
71A GLY* 1.3 78.7 - - - +
73A ILE* 1.3 64.2 + - - -
93A PHE* 3.7 2.7 - - - -
94A PRO 3.4 12.1 - - - -
258A LEU* 3.6 19.5 - - - -
262A VAL* 4.1 3.4 - - - -
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Residues in contact with ILE 73 (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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12A GLY 3.3 9.0 - - - +
14A VAL* 3.8 22.4 - - + -
61A VAL* 4.1 15.0 - - + -
64A MSE 3.3 31.6 - - + -
65A VAL* 4.3 5.8 - - + -
72A GLY* 1.3 75.1 - - - -
74A ILE* 1.3 67.6 + - - +
75A LEU* 4.4 3.4 - - + +
88A LEU* 3.7 32.5 - - + -
93A PHE* 3.5 19.7 - - + -
94A PRO 3.2 6.1 + - - -
95A PHE* 3.1 11.7 - - + +
96A VAL 3.0 23.9 + - - -
258A LEU* 3.4 8.5 - - - +
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Residues in contact with ILE 74 (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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11A LEU* 5.0 4.9 - - + -
12A GLY 2.7 15.8 + - - +
13A LEU* 3.6 9.7 - - + -
14A VAL 3.1 23.6 + - - -
35A ILE* 3.8 37.5 - - + -
73A ILE* 1.3 74.5 - - - +
75A LEU* 1.3 61.2 + - - +
76A LEU* 3.7 21.7 + - + +
96A VAL* 3.5 9.4 - - + +
98A ILE* 4.0 15.9 - - + -
254A ALA* 4.2 8.7 - - + -
255A ALA* 4.0 22.4 - - + +
258A LEU* 3.5 23.8 - - + -
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Residues in contact with LEU 75 (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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14A VAL* 3.6 20.2 - - + -
73A ILE* 4.0 8.5 - - + -
74A ILE* 1.3 72.8 - - - +
76A LEU* 1.3 57.7 + - - +
77A TYR* 3.0 41.2 + - + +
82A ASP* 4.4 2.2 - - - +
84A ILE* 4.0 16.2 - - + -
85A ILE* 3.5 31.9 - - + -
88A LEU* 4.7 3.1 - - + -
95A PHE* 4.3 14.4 - - + -
96A VAL 2.9 11.1 + - - +
97A LEU* 3.6 23.8 - - + -
98A ILE* 2.9 30.5 + - - +
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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