Contacts of the strand formed by residues 1300 - 1305 (chain U) in PDB entry 6FF7
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 GLY1300 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170U ASN* 5.7 6.1 - - - -
1176U ASP* 3.4 9.6 - - - -
1269U ASP 2.9 8.8 + - - -
1270U TYR* 3.3 8.5 - - - +
1271U ILE 2.8 27.3 + - - -
1297U ALA* 3.2 10.3 - - - +
1299U LEU* 1.3 79.7 - - - +
1301U LEU* 1.3 60.4 + - - -
1302U TYR 4.3 0.2 - - - -
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Residues in contact with LEU1301 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143U LEU* 5.9 6.5 - - + -
1176U ASP 3.2 7.5 + - - -
1177U PHE* 3.0 35.1 - - + +
1178U GLN 3.2 4.5 + - - +
1271U ILE* 3.6 7.0 - - + +
1294U MET* 5.8 5.4 - - - +
1297U ALA* 4.1 13.2 - - + -
1300U GLY* 1.3 73.3 - - - +
1302U TYR* 1.3 60.9 + - - +
1303U ILE* 4.2 0.9 - - + -
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Residues in contact with TYR1302 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178U GLN* 3.6 10.8 - - + +
1210U LEU* 6.4 2.7 - - + -
1271U ILE 3.0 11.9 + - - +
1272U LEU* 3.5 6.9 - - + +
1273U LEU* 2.8 27.8 + - - +
1300U GLY 4.3 0.4 - - - -
1301U LEU* 1.3 74.6 - - - +
1303U ILE* 1.3 60.2 + - - +
1304U PHE 4.2 0.2 + - - -
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Residues in contact with ILE1303 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178U GLN 2.9 13.5 + - - +
1179U LEU* 4.4 9.9 - - + -
1180U ILE* 2.6 37.9 + - - +
1273U LEU* 3.3 15.3 - - + +
1301U LEU 5.7 0.7 - - - -
1302U TYR* 1.3 74.1 - - - +
1304U PHE* 1.3 57.9 + - - +
1305U ALA* 4.1 3.6 - - + -
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Residues in contact with PHE1304 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180U ILE* 3.5 11.9 - - + +
1182U VAL* 5.2 4.7 - - + -
1203U GLU* 4.5 28.5 - - + +
1206U TYR* 5.4 6.3 - - + -
1207U VAL* 5.6 5.8 - - + +
1273U LEU 2.7 14.0 + - - +
1274U SER* 3.6 4.6 - - - -
1275U LEU 3.0 25.1 + - - -
1276U VAL 4.3 1.7 + - - -
1302U TYR 5.6 0.4 - - - +
1303U ILE* 1.3 73.6 - - - +
1305U ALA* 1.3 62.2 + - - +
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Residues in contact with ALA1305 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180U ILE 3.1 10.8 + - - +
1181U ASN* 3.3 2.3 - - - -
1182U VAL* 3.1 26.7 + - - +
1203U GLU* 6.0 1.1 - - - -
1275U LEU* 3.7 22.7 - - + -
1276U VAL 5.3 3.1 - - - +
1277U ARG 5.7 0.4 - - - +
1303U ILE* 4.1 3.9 + - + -
1304U PHE* 1.3 76.3 - - - +
1306U ARG* 1.3 67.0 + - - +
1307U VAL* 3.1 9.9 + - - +
1310U PHE* 5.9 5.6 - - + -
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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