Contacts of the strand formed by residues 7 - 12 (chain D) in PDB entry 4OIP
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 LYS 7 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102C LEU* 2.9 37.5 + - + +
1103C ASP 3.7 10.8 - - - +
1104C GLU* 3.5 20.8 + - - +
1106C ASP* 2.5 37.2 + - - +
5D VAL* 3.3 8.4 + - - +
6D ARG* 1.3 91.4 - - - +
8D VAL* 1.3 71.2 + - - +
1456D LYS* 4.8 11.5 - - + +
1457D ASP 3.4 7.9 - - - +
1458D GLU* 3.2 38.1 + - - +
1459D LEU* 4.1 2.4 - - - +
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Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085C PHE* 4.7 4.0 - - + -
1099C VAL* 3.8 21.1 - - + -
1100C GLN 3.3 8.7 - - - +
1101C THR* 3.8 14.4 - - + -
7D LYS* 1.3 82.1 - - - +
9D ARG* 1.3 61.0 + - - +
1434D TRP* 3.4 30.2 + - + -
1435D LEU* 4.5 10.1 - - + -
1456D LYS* 4.4 1.8 - - - -
1457D ASP* 2.7 37.2 + - + +
1459D LEU* 4.6 3.6 - - + -
1468D LEU* 3.8 36.1 - - + -
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Residues in contact with ARG 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098C ASP* 3.4 7.2 + - - +
1099C VAL* 3.4 2.4 - - - +
1100C GLN* 2.6 75.4 + - - +
1102C LEU* 3.7 31.8 - - + +
1106C ASP* 4.7 6.7 + - - +
1108C PRO* 5.5 4.0 - - - +
7D LYS 4.4 0.2 - - - -
8D VAL* 1.3 73.5 - - - +
10D ILE* 1.3 66.0 + - - +
11D ALA* 4.8 11.9 - - + +
1434D TRP* 4.5 2.0 - - - -
1454D GLY* 3.8 11.0 - - - +
1455D LYS 3.4 13.9 - - - +
1456D LYS* 3.6 25.0 - - + +
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Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092C LEU* 4.6 3.1 - - + -
1097C LEU* 3.9 27.1 - - + -
1098C ASP 3.3 7.4 - - - +
1099C VAL* 4.3 12.3 - - + -
9D ARG* 1.3 75.0 - - - +
11D ALA* 1.3 64.8 + - - +
1434D TRP* 3.5 40.6 - - + +
1447D LEU* 3.9 32.5 - - + +
1450D ALA* 3.3 22.1 - - + +
1451D ALA* 4.0 7.2 - - + -
1454D GLY* 3.3 22.7 - - - -
1455D LYS 3.1 5.6 + - - +
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C LEU* 3.8 3.8 - - - -
1098C ASP* 2.8 39.1 + - + +
9D ARG* 4.8 14.4 - - - +
10D ILE* 1.3 78.3 - - - +
12D LEU* 1.3 67.1 + - - +
507D ASN* 4.1 14.4 - - - +
1451D ALA* 3.4 16.8 - - - +
1454D GLY* 4.3 6.3 - - - -
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096C ALA* 4.5 8.7 - - + +
1097C LEU* 4.6 4.7 - - + -
1098C ASP* 4.7 2.4 - - - +
11D ALA* 1.3 79.9 - - - +
13D ALA* 1.3 63.2 + - - +
14D SER 3.9 0.4 + - - -
17D LYS* 6.0 0.9 - - - -
101D HIS* 6.2 1.1 - - + -
104D PHE* 3.5 34.5 - - + -
502D PHE* 3.6 32.3 - - + -
507D ASN* 3.9 10.7 - - + +
508D ARG 4.3 0.9 - - - +
511D TRP* 3.6 56.7 - - + +
512D MET* 3.9 14.6 - - + -
1451D ALA* 3.4 12.6 + - + +
1452D ILE* 4.7 2.9 - - + -
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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