Contacts of the strand formed by residues 8 - 12 (chain A) in PDB entry 4EFH
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 LEU 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ALA* 1.3 75.0 - - - +
9A VAL* 1.3 61.0 + - - +
10A ILE* 4.2 4.0 - - + -
20A GLY 3.5 6.5 - - - +
21A PHE* 3.6 35.7 - - + -
90A PHE* 3.7 22.9 - - + -
94A LEU* 4.4 9.9 - - + -
96A VAL* 3.7 26.2 - - + -
98A PRO* 4.8 2.2 - - + -
101A HIS* 3.6 35.7 - - + +
102A PRO 2.8 10.0 + - - +
103A VAL* 3.8 14.6 - - + -
104A LEU* 2.7 31.4 + - - +
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Residues in contact with VAL 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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8A LEU* 1.3 79.1 - - - +
10A ILE* 1.3 65.8 + - - +
19A ALA* 3.3 1.9 - - - -
20A GLY 2.9 33.2 + - - +
21A PHE 4.6 0.2 - - - -
22A ALA* 3.8 27.1 - - + +
104A LEU* 3.5 10.5 - - + +
106A THR* 5.3 4.9 - - + -
340A TRP* 3.1 46.6 + - + +
343A GLY* 3.8 30.1 - - - +
344A SER* 3.8 4.5 - - - +
347A ALA* 4.3 4.7 - - + -
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Residues in contact with ILE 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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8A LEU* 4.9 3.8 - - + -
9A VAL* 1.3 80.7 - - - +
11A ASP* 1.3 62.3 + - - +
12A ASN* 3.2 27.3 + - - +
17A CYS* 5.5 4.5 - - + -
18A LYS 3.6 6.7 - - - +
19A ALA* 4.5 2.7 - - + -
86A TRP* 4.1 12.1 - - + +
89A THR* 3.7 30.5 - - + +
90A PHE* 3.6 36.8 - - + -
94A LEU* 5.2 2.0 - - + -
103A VAL* 4.1 13.5 - - + -
104A LEU 2.8 9.7 + - - -
105A LEU* 3.5 14.6 - - + -
106A THR* 3.0 28.9 + - - +
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Residues in contact with ASP 11 (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 VAL* 4.1 1.2 - - + -
10A ILE* 1.3 72.2 - - - +
12A ASN* 1.3 61.1 + - - +
13A GLY* 3.4 3.8 + - - -
16A MET 3.9 0.3 - - - +
17A CYS* 3.4 4.5 - - - +
18A LYS* 2.8 72.0 + - + +
106A THR* 2.7 29.4 + - + +
137A GLN* 3.7 9.0 + - - +
337A TYR* 6.2 0.2 - - - -
339A VAL* 3.3 33.4 - - + +
340A TRP* 4.0 14.4 + - + +
403A ADP 5.1 1.9 + - - -
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Residues in contact with ASN 12 (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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10A ILE* 3.2 22.4 + - - +
11A ASP* 1.3 71.4 - - - +
13A GLY* 1.3 63.0 + - - +
17A CYS* 3.9 10.4 - - - -
71A ILE* 3.7 26.5 - - + +
74A GLY* 5.4 2.1 - - - +
82A MET* 3.6 9.4 - - + +
85A ILE* 5.1 0.2 - - - +
86A TRP* 2.6 40.9 + - - +
105A LEU* 4.5 3.6 - - - +
106A THR* 3.2 28.5 + - - +
119A MET* 4.7 1.0 - - - +
137A GLN* 3.5 18.0 + - - -
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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