Contacts of the strand formed by residues 7 - 12 (chain N) in PDB entry 5X22
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101M THR* 3.4 1.9 - - - -
1102M LEU* 2.6 52.3 + - + +
1103M ASP 4.0 9.2 - - - +
1104M GLU* 4.4 13.0 + - - +
1106M ASP* 2.7 35.1 + - - +
5N VAL* 3.4 4.0 - - - +
6N ARG* 1.3 84.8 - - + +
8N VAL* 1.3 68.8 + - - +
1456N LYS* 4.1 20.2 - - + +
1457N ASP 3.4 11.7 - - - +
1458N GLU* 3.3 37.1 + - - +
1459N LEU* 3.8 2.6 - - - +
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Residues in contact with VAL 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085M PHE* 4.7 6.1 - - + -
1099M VAL* 3.8 21.1 - - + -
1100M GLN 3.2 5.6 - - - +
1101M THR* 4.2 9.4 - - + -
5N VAL* 4.8 0.2 - - + -
7N LYS* 1.3 81.2 - - - +
9N ARG* 1.3 61.3 + - - +
1434N TRP* 3.2 27.4 + - + -
1435N LEU* 4.1 17.0 - - + -
1456N LYS* 4.1 1.6 - - - -
1457N ASP* 2.5 40.2 + - + -
1459N LEU* 4.1 9.4 - - + -
1468N LEU* 3.7 31.0 - - + -
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Residues in contact with ARG 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098M ASP* 3.5 6.1 + - - +
1099M VAL* 3.2 5.4 - - - +
1100M GLN* 2.6 79.4 + - + +
1102M LEU* 4.0 24.2 - - + +
1106M ASP* 5.4 3.8 + - - +
1108M PRO* 5.9 3.0 - - - +
7N LYS 4.3 0.2 - - - -
8N VAL* 1.3 73.5 - - - +
10N ILE* 1.3 67.7 + - - +
11N ALA* 5.1 9.8 - - - +
17N LYS* 6.0 0.8 - - - +
1434N TRP* 4.4 2.0 - - - -
1454N GLY* 3.9 12.3 - - - +
1455N LYS 3.3 7.6 - - - +
1456N LYS* 3.6 29.0 - - + +
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Residues in contact with ILE 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092M LEU* 4.7 3.6 - - + -
1097M LEU* 4.1 24.5 - - + -
1098M ASP 3.2 8.7 - - - +
1099M VAL* 4.0 13.0 - - + -
9N ARG* 1.3 75.4 - - - +
11N ALA* 1.3 63.3 + - - +
1434N TRP* 3.4 41.5 - - + +
1447N LEU* 3.7 32.5 - - + +
1450N ALA* 3.5 21.7 - - + +
1451N ALA* 4.0 7.6 - - + -
1454N GLY* 3.2 22.2 - - - -
1455N LYS 3.0 7.6 + - - +
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Residues in contact with ALA 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097M LEU* 3.7 3.3 - - - -
1098M ASP* 2.8 37.9 + - + +
9N ARG* 5.1 12.3 - - + +
10N ILE* 1.3 78.9 - - - +
12N LEU* 1.3 65.4 + - - +
507N ASN* 4.1 12.1 - - - +
1451N ALA* 3.2 17.3 - - - +
1454N GLY* 4.1 9.9 - - - -
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Residues in contact with LEU 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096M ALA 4.5 4.0 - - - +
1097M LEU* 4.7 5.6 - - + -
1098M ASP* 4.8 3.3 - - - +
11N ALA* 1.3 79.2 - - - +
13N ALA* 1.3 61.6 + - - +
14N SER 3.9 2.3 + - - -
17N LYS* 6.0 1.2 - - - -
104N PHE* 3.5 33.9 - - + -
502N PHE* 3.7 34.5 - - + -
507N ASN* 3.9 24.5 - - + +
511N TRP* 3.8 36.7 - - + +
512N MET* 4.1 10.3 - - + +
1451N ALA* 3.1 12.9 + - + +
1452N ILE* 4.1 18.4 - - + -
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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