Contacts of the strand formed by residues 1224 - 1232 (chain A) 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 ARG1224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1199A LYS* 5.7 2.3 - - - +
1215A ASN* 4.8 12.8 - - + -
1216A LEU 3.4 13.2 - - - +
1217A GLN* 3.8 8.0 - - + +
1222A LYS 4.0 1.4 + - - -
1223A GLU* 1.3 80.1 - - - +
1225A THR* 1.3 59.4 + - - +
1226A ALA 5.3 1.1 - - - +
592T GLU 4.3 6.4 + - - +
593T TYR* 5.0 11.2 + - - +
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Residues in contact with THR1225 (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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960A ASN* 5.3 10.8 - - - -
1198A PRO* 4.3 1.6 - - - +
1199A LYS* 3.4 29.0 + - - +
1216A LEU 2.9 13.1 + - - -
1217A GLN* 4.8 1.3 - - - -
1218A ASN* 4.6 20.0 - - - -
1223A GLU 4.6 0.7 - - - -
1224A ARG* 1.3 75.8 - - - +
1226A ALA* 1.3 61.0 + - - +
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Residues in contact with ALA1226 (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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960A ASN* 5.7 5.8 - - + -
1196A ILE* 5.2 8.1 - - + -
1197A LEU 3.7 14.1 - - - +
1198A PRO* 4.0 11.2 - - + -
1199A LYS* 4.3 3.1 - - - +
1215A ASN* 3.9 6.9 - - - +
1216A LEU* 3.3 33.1 + - + +
1224A ARG* 5.3 0.9 - - - +
1225A THR* 1.3 82.0 + - - +
1227A GLN* 1.3 64.9 + - - +
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Residues in contact with GLN1227 (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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1195A ARG 3.5 0.7 - - - +
1196A ILE* 3.3 6.6 - - - +
1197A LEU* 2.9 46.1 + - + +
1206A GLU* 6.0 5.2 - - + -
1208A THR* 5.1 13.2 - - - -
1213A VAL 4.7 6.1 - - - +
1215A ASN* 4.6 6.5 - - + +
1216A LEU* 5.4 1.1 - - - -
1226A ALA* 1.3 74.5 - - - +
1228A CYS* 1.3 61.7 + - - +
1229A PHE 4.1 0.9 - - - +
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Residues in contact with CYS1228 (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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952A VAL* 6.1 4.0 - - + -
956A CYS* 5.8 8.5 - - + -
1194A CYS* 5.4 6.7 - - + -
1195A ARG 3.2 9.0 - - - +
1196A ILE* 5.3 2.5 - - + -
1212A GLY 4.2 0.9 - - - +
1213A VAL* 3.2 25.6 + - - +
1214A TRP 3.5 19.9 + - - +
1215A ASN 5.7 1.3 - - - -
1216A LEU* 5.8 4.5 - - + -
1227A GLN* 1.3 74.4 - - - +
1229A PHE* 1.3 61.9 + - - +
1230A LEU* 4.0 2.3 + - - +
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Residues in contact with PHE1229 (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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1194A CYS* 3.1 4.5 - - - -
1195A ARG* 2.9 39.0 + - + +
1197A LEU* 6.5 1.6 - - + -
1212A GLY 4.5 3.8 - - - -
1213A VAL* 5.1 2.5 - - - +
1227A GLN* 4.1 1.6 - - + -
1228A CYS* 1.3 72.6 - - - +
1230A LEU* 1.3 59.2 + - - +
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Residues in contact with LEU1230 (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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1192A PHE* 6.5 0.4 - - + -
1193A GLU 3.5 9.0 - - - +
1194A CYS* 4.2 7.4 - - + +
1212A GLY 3.8 17.3 + - - +
1228A CYS 5.1 2.0 - - - +
1229A PHE* 1.3 75.2 - - - +
1231A ARG* 1.3 62.7 + - - +
1276A GLU* 5.4 2.2 - - + +
1277A ALA* 4.9 17.0 - - + +
1280A ASN* 3.3 26.0 - - - +
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Residues in contact with ARG1231 (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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1133A CYS* 5.5 13.2 - - + +
1192A PHE* 3.7 5.2 - - - +
1193A GLU* 2.8 36.0 + - + +
1230A LEU* 1.3 74.8 - - - +
1232A VAL* 1.3 65.2 + - - +
1277A ALA* 4.7 8.4 - - - +
1280A ASN* 5.4 1.3 - - + -
1281A THR* 4.9 14.8 - - - +
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Residues in contact with VAL1232 (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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1133A CYS* 5.7 4.0 - - - +
1192A PHE* 4.2 9.9 - - + -
1193A GLU* 5.5 0.7 - - - -
1231A ARG* 1.3 79.4 - - - +
1233A ASP* 1.3 69.0 + - - +
1234A ASP* 3.8 0.9 + - - -
1236A SER* 5.3 6.3 - - - -
1237A MET* 5.7 4.3 - - + +
1274A PHE* 6.0 3.4 - - + -
1277A ALA* 4.6 10.5 + - + +
1281A THR* 4.1 21.9 - - - -
1284A LEU* 5.2 8.5 - - + -
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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