Contacts of the strand formed by residues 1258 - 1261 (chain A) in PDB entry 1FP7
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 ASN1258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A K 3.2 7.1 - - - -
1041A ALA 3.1 4.7 - - - +
1042A LYS* 2.8 25.1 - - - +
1129A PHE* 3.6 18.9 - - + -
1130A THR* 2.6 27.5 + - + +
1132A ASP* 2.7 26.5 + - - -
1256A LYS 4.2 1.0 + - - -
1257A PRO* 1.3 76.7 - - - +
1259A LEU* 1.3 61.7 + - - +
1260A VAL* 3.8 2.6 + - + +
1268A ALA 3.7 0.3 - - - +
1269A PHE* 3.5 8.3 - - - -
1270A ILE 2.8 44.8 + - - +
1271A HIS* 4.2 2.6 - - - +
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Residues in contact with LEU1259 (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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1019A VAL* 3.7 30.1 - - + +
1022A LEU* 4.6 7.6 - - + -
1023A ALA* 4.3 8.3 - - + +
1026A LEU* 5.1 3.8 - - + -
1028A ILE* 4.2 13.2 - - + -
1033A VAL* 6.5 0.2 - - + -
1040A LYS* 3.6 1.9 - - - -
1041A ALA* 2.6 37.6 + - + +
1043A ILE* 3.6 27.4 - - + -
1093A MET* 4.0 16.6 - - + -
1257A PRO 4.1 0.6 + - - -
1258A ASN* 1.3 71.2 - - - +
1260A VAL* 1.3 85.3 + - - +
1267A PRO* 4.3 6.7 - - + -
1268A ALA 3.2 24.0 - - - +
1269A PHE* 4.4 3.1 - - + -
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Residues in contact with VAL1260 (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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1019A VAL* 4.3 5.2 - - - -
1022A LEU* 4.9 0.9 - - - -
1039A TYR 3.1 22.2 - - - +
1040A LYS* 3.7 17.9 - - + -
1119A VAL* 3.7 19.3 - - + -
1120A VAL 3.3 13.7 - - - +
1121A PRO* 4.3 1.1 - - + -
1125A ILE* 4.4 1.3 - - + -
1129A PHE* 4.1 25.8 - - + -
1258A ASN* 4.5 3.1 - - + +
1259A LEU* 1.3 91.0 - - - +
1261A GLN* 1.3 59.8 + - - +
1268A ALA* 2.7 38.5 + - - +
1270A ILE* 4.2 11.9 - - + -
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Residues in contact with GLN1261 (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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1016A MET* 2.9 22.7 - - + +
1017A LYS* 2.7 43.6 + - - +
1019A VAL* 4.0 8.0 - - - +
1022A LEU* 2.9 34.0 - - + +
1039A TYR* 4.9 2.7 - - - +
1119A VAL* 2.9 7.1 - - - +
1120A VAL* 2.7 38.3 + - + +
1260A VAL* 1.3 75.1 - - - +
1262A THR* 1.3 65.4 - - - +
1265A ASN* 2.9 19.9 + - - -
1266A THR 3.1 16.4 - - - +
1268A ALA* 4.2 0.7 - - - +
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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