Contacts of the strand formed by residues 1297 - 1300 (chain A) in PDB entry 2QOM
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 ARG1297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1029A MET* 3.5 30.5 + - - +
1030A GLY* 6.4 0.4 - - - -
1031A ASP 5.0 2.9 - - - -
1032A LEU* 3.6 9.9 - - - -
1035A ILE* 3.6 22.6 - - - +
1039A ALA 4.5 3.6 + - - -
1040A GLY* 3.9 15.2 - - - -
1041A ALA 3.5 8.0 + - - +
1042A TRP* 3.7 18.5 - - + -
1068A ASP* 3.1 32.9 + - - -
1070A LYS* 5.6 0.4 - - - +
1079A PHE* 3.6 22.4 - - - -
1271A ASN 3.1 6.8 - - - +
1272A VAL* 3.4 2.3 - - - +
1273A ARG* 2.7 45.2 + - + +
1295A ASN* 5.3 0.4 - - + +
1296A PHE* 1.3 78.2 - - - +
1298A TYR* 1.3 61.0 + - - +
1299A SER* 3.0 24.4 + - - +
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Residues in contact with TYR1298 (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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1040A GLY* 3.7 0.2 - - - -
1041A ALA* 3.0 39.8 + - + +
1271A ASN* 3.7 17.2 + - + -
1272A VAL* 4.5 15.5 - - + +
1296A PHE* 4.1 16.6 - + + -
1297A ARG* 1.3 69.2 - - - +
1299A SER* 1.3 58.5 + - - +
1300A PHE* 3.3 49.6 - + + +
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Residues in contact with SER1299 (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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1035A ILE* 3.3 33.2 - - - +
1036A ASN 4.3 5.0 - - - +
1039A ALA 3.9 9.0 - - - -
1040A GLY* 4.4 0.9 - - - -
1270A ASP 4.4 1.3 - - - +
1271A ASN* 2.7 52.4 + - - +
1273A ARG* 5.3 1.0 - - - +
1297A ARG* 3.0 33.7 + - - +
1298A TYR* 1.3 71.6 - - - +
1300A PHE* 1.3 53.2 + - - +
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Residues in contact with PHE1300 (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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1037A GLY* 3.3 7.3 - - - -
1038A GLU 3.3 4.2 + - - -
1039A ALA* 2.8 44.0 + - + +
1040A GLY* 3.6 28.9 - - - -
1041A ALA* 4.1 4.7 - - + -
1067A VAL* 6.5 0.2 - - + -
1271A ASN* 3.7 13.2 - - - +
1298A TYR* 3.3 49.6 - + + +
1299A SER* 1.3 74.8 - - - +
1301A GLY* 1.3 62.5 + - - +
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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