Contacts of the strand formed by residues 4 - 10 (chain A) in PDB entry 4MDH
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 ILE 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLU 4.3 2.2 - - - +
3A PRO* 1.3 78.5 - - - +
5A ARG* 1.3 64.6 + - - +
6A VAL* 3.8 22.0 - - + -
29A PHE* 3.9 31.2 - - + -
33A GLN* 4.1 21.3 - - + +
34A PRO 3.1 9.1 + - - +
35A ILE* 3.5 5.5 - - + +
36A ILE* 3.0 22.7 + - - -
81A ASP* 3.4 25.8 - - + +
82A VAL* 4.7 1.8 - - + -
257A TRP* 4.1 19.3 - - + -
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Residues in contact with ARG 5 (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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4A ILE* 1.3 75.7 - - - +
6A VAL* 1.3 60.3 + - - +
36A ILE* 3.4 36.6 - - + +
38A VAL* 3.3 27.6 - - + +
68A ILE* 4.1 11.7 - - - +
75A ILE* 4.3 12.3 + - - +
78A LYS* 3.5 22.6 + - - +
79A ASP* 3.7 27.1 + - - +
80A LEU* 3.8 11.1 - - + +
81A ASP* 2.8 36.9 + - - +
82A VAL 3.4 7.4 + - - +
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Residues in contact with VAL 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.8 22.2 - - + -
5A ARG* 1.3 79.1 - - - +
7A LEU* 1.3 64.4 + - - +
8A VAL* 4.7 2.7 - - + -
23A ILE* 4.9 5.2 - - + -
29A PHE* 3.9 17.3 - - + -
35A ILE* 3.5 25.4 - - + -
36A ILE 3.2 4.9 + - - -
37A LEU* 3.6 11.0 - - + +
38A VAL* 2.8 28.1 + - - +
80A LEU* 4.4 2.2 - - - -
82A VAL* 3.5 16.6 - - + -
84A ILE* 4.0 26.7 - - + -
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Residues in contact with LEU 7 (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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6A VAL* 1.3 73.5 - - - +
8A VAL* 1.3 68.9 + - - +
9A THR* 3.8 13.9 - - + -
38A VAL* 3.6 17.3 - - + +
40A LEU* 4.1 12.3 - - + -
76A ALA* 3.2 36.3 - - + +
77A PHE* 3.3 42.6 - - + -
80A LEU* 3.5 21.5 - - + +
82A VAL 3.1 9.3 + - - +
83A ALA* 4.1 4.3 - - + -
84A ILE* 2.8 32.1 + - - +
85A LEU* 4.2 5.6 - - + -
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Residues in contact with VAL 8 (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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6A VAL* 4.7 2.9 - - + -
7A LEU* 1.3 80.0 - - - +
9A THR* 1.3 74.2 + - - +
11A ALA* 3.4 6.8 - - - +
16A ALA* 4.5 15.0 - - + -
19A LEU* 4.3 14.6 - - + -
20A LEU* 4.2 7.6 - - + -
23A ILE* 3.9 27.8 - - + -
37A LEU* 4.2 14.4 - - + -
38A VAL 3.1 9.5 + - - -
39A LEU* 3.8 10.2 - - + -
40A LEU 3.1 19.2 + - - -
84A ILE* 3.6 8.5 - - + +
86A VAL* 4.2 14.4 - - + -
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Residues in contact with THR 9 (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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7A LEU* 3.8 17.5 - - + -
8A VAL* 1.3 75.3 - - - +
10A GLY* 1.3 70.5 + - - +
11A ALA 3.0 2.4 + - - -
40A LEU* 3.6 25.1 - - + -
77A PHE* 4.2 1.1 - - + -
84A ILE 3.0 8.7 + - - -
85A LEU* 3.1 30.2 - - + +
86A VAL* 3.2 26.3 + - - +
87A GLY* 3.0 21.6 + - - -
111A GLN* 4.1 8.9 + - - +
335A NAD 4.4 7.2 - - - -
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Residues in contact with GLY 10 (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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9A THR* 1.3 77.5 + - - +
11A ALA* 1.4 57.7 + - - +
12A ALA 3.2 7.4 + - - -
13A GLY* 3.4 9.3 + - - -
16A ALA* 3.1 16.8 + - - +
40A LEU 2.9 7.0 + - - -
41A ASP* 3.4 12.8 - - - -
86A VAL* 4.8 3.3 - - - +
87A GLY* 3.6 7.6 - - - -
335A NAD 3.5 30.9 + - - +
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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