Contacts of the strand formed by residues 1197 - 1206 (chain r) 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 THR1197 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1192r PRO* 4.1 0.7 - - - +
1193r ILE* 2.9 29.0 + - - +
1194r THR* 3.0 19.9 + - - +
1196r SER* 1.3 81.2 - - - +
1198r LEU* 1.3 62.0 + - - +
1255r PHE* 5.1 8.5 - - - -
1256r VAL 3.5 11.2 - - - -
1257r PRO* 4.8 1.3 - - - -
1258r VAL* 5.4 1.1 - - - -
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Residues in contact with LEU1198 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190r LEU* 5.9 3.6 - - + -
1191r GLN 3.8 10.8 - - - +
1192r PRO* 4.2 7.6 - - + -
1193r ILE* 4.9 2.2 - - - -
1197r THR* 1.3 73.5 - - - +
1199r LYS* 1.3 63.6 + - - +
1200r VAL* 5.5 0.4 - - - +
1255r PHE* 3.3 7.2 - - - +
1256r VAL* 2.9 38.2 + - + +
1257r PRO 5.2 1.2 - - - -
1258r VAL* 5.8 4.2 - - + +
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Residues in contact with LYS1199 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189r HIS 3.7 1.0 - - - +
1190r LEU* 3.3 7.4 - - - +
1191r GLN* 2.9 42.8 + - + +
1193r ILE* 4.8 8.7 - - + +
1198r LEU* 1.3 74.4 - - - +
1200r VAL* 1.3 60.0 + - - +
1254r PHE 4.0 4.5 - - - +
1255r PHE* 4.5 4.7 - - + +
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Residues in contact with VAL1200 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1188r VAL* 5.9 4.9 - - + -
1189r HIS 3.7 3.1 - - - -
1190r LEU* 4.7 4.3 - - + +
1198r LEU 4.2 1.1 + - - +
1199r LYS* 1.3 74.3 - - - +
1201r GLU* 1.3 60.4 + - - +
1202r LEU* 3.9 2.9 - - + +
1252r ILE 3.6 1.6 - - - +
1253r THR* 3.4 4.8 - - - -
1254r PHE* 2.9 44.0 + - + +
1256r VAL* 5.9 4.5 - - + +
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Residues in contact with GLU1201 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187r SER 3.7 0.3 - - - +
1188r VAL* 3.3 6.0 - - - +
1189r HIS* 2.9 48.2 + - + +
1200r VAL* 1.3 71.7 - - - +
1202r LEU* 1.3 62.8 + - - +
1203r THR* 3.8 1.7 + - - -
1251r LEU* 6.3 3.1 - - + -
1252r ILE 3.5 5.4 - - - +
1253r THR* 4.5 7.2 - - - +
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Residues in contact with LEU1202 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186r LEU* 6.0 3.8 - - + -
1187r SER 3.4 6.5 - - - +
1188r VAL* 4.6 4.9 - - + +
1200r VAL* 3.9 4.4 - - + +
1201r GLU* 1.3 72.2 - - - +
1203r THR* 1.3 62.4 + - - +
1204r ILE* 3.8 1.7 + - + +
1250r HIS 3.5 1.6 - - - +
1251r LEU* 3.5 4.2 - - - +
1252r ILE* 2.8 47.3 + - + +
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Residues in contact with THR1203 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1185r GLU 3.7 0.2 - - - +
1186r LEU* 3.3 7.3 - - - +
1187r SER* 2.7 45.5 + - - -
1201r GLU 3.8 2.0 + - - -
1202r LEU* 1.3 72.3 - - - +
1204r ILE* 1.3 62.6 - - - +
1205r THR* 3.6 3.6 + - - -
1249r GLU* 5.5 7.2 - - - -
1250r HIS 3.6 5.8 - - - -
1251r LEU* 4.8 3.6 - - - +
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Residues in contact with ILE1204 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184r LEU* 5.4 8.7 - - + -
1185r GLU 3.7 4.9 - - - +
1186r LEU* 4.6 5.6 - - + -
1202r LEU* 3.8 2.5 + - + +
1203r THR* 1.3 71.3 - - - +
1205r THR* 1.3 60.6 + - - +
1206r PRO 4.1 0.9 - - - -
1248r ASP 4.2 1.2 - - - +
1249r GLU* 3.1 6.1 - - - -
1250r HIS* 2.9 44.7 + - + +
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Residues in contact with THR1205 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184r LEU* 4.8 2.0 - - - +
1185r GLU* 2.8 42.8 + - - +
1203r THR* 3.6 3.3 + - - -
1204r ILE* 1.3 73.6 - - - +
1206r PRO* 1.3 66.5 - - - +
1207r ASP* 3.2 0.9 + - - +
1249r GLU* 4.4 15.3 - - - +
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Residues in contact with PRO1206 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183r LYS 4.0 4.5 - - - +
1184r LEU* 4.8 2.9 - - + -
1204r ILE 4.1 2.2 - - - -
1205r THR* 1.3 71.3 - - - +
1207r ASP* 1.3 60.5 + - - +
1208r PHE 3.5 6.8 - - - +
1246r ALA* 4.4 9.4 - - + -
1247r GLN* 3.5 35.8 - - - +
1248r ASP 5.0 5.8 - - - +
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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