Contacts of the strand formed by residues 1189 - 1194 (chain F) in PDB entry 6X34
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 LEU1189 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1077F ALA* 3.9 21.5 - - + +
1078F GLU 4.5 8.3 - - - +
1081F TYR 4.8 6.7 - - - +
1082F ALA* 4.9 2.0 - - + -
1104F TRP* 4.6 2.9 - - - -
1105F ALA* 2.6 39.8 + - - +
1107F PRO* 4.2 19.8 - - + +
1188F PHE* 1.3 74.2 - - - +
1190F PRO* 1.3 73.3 - - + +
1226F PHE* 5.5 0.9 - - - -
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Residues in contact with PRO1190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076F ARG* 3.9 1.6 - - - +
1077F ALA* 3.6 30.0 + - + +
1081F TYR 6.1 0.2 - - - +
1090F PHE* 3.6 33.2 - - + -
1103F GLY 4.5 3.6 - - - +
1104F TRP* 3.9 24.7 - - + -
1188F PHE 4.5 0.2 - - - +
1189F LEU* 1.3 91.7 - - + +
1191F VAL* 1.3 59.5 + - - +
1192F CYS* 5.8 0.4 - - - -
1204F LEU* 6.5 0.4 - - + -
1226F PHE* 4.1 32.3 - - + -
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Residues in contact with VAL1191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074F ILE* 5.0 6.1 - - + -
1075F PHE 3.3 15.0 - - - +
1076F ARG* 3.9 18.2 - - + +
1090F PHE* 4.0 8.7 - - - -
1101F ARG 4.7 1.6 - - - +
1102F VAL* 4.7 1.3 - - - -
1103F GLY 3.3 29.8 + - - +
1105F ALA* 3.7 25.4 - - + -
1109F LEU* 5.1 5.4 - - + -
1115F LEU* 3.8 31.9 - - + -
1122F TYR 4.6 1.3 - - - +
1189F LEU 3.7 0.4 + - - -
1190F PRO* 1.3 76.3 - - - +
1192F CYS* 1.3 77.6 + - - +
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Residues in contact with CYS1192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839F LEU* 4.1 8.3 - - + -
1074F ILE* 3.3 4.3 - - - -
1075F PHE* 2.5 56.8 + - + +
1090F PHE* 3.5 25.1 - - - -
1092F PHE* 3.9 18.2 - - + -
1101F ARG 4.3 6.1 - - - -
1102F VAL* 5.8 0.4 - - - +
1115F LEU* 4.8 1.7 - - - +
1191F VAL* 1.3 86.2 - - - +
1193F SER* 1.3 59.2 + - - +
1202F LEU* 3.7 23.6 - - - -
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Residues in contact with SER1193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072F VAL* 5.5 7.6 - - - -
1073F ARG 3.3 9.6 - - - -
1074F ILE* 5.1 2.2 - - - -
1075F PHE* 4.8 1.8 - - - -
1092F PHE* 4.6 6.1 - - - -
1100F MET* 3.6 23.6 - - - +
1101F ARG* 2.6 53.6 + - - +
1115F LEU* 4.2 10.3 - - - -
1192F CYS* 1.3 77.2 - - - +
1194F LEU* 1.3 60.6 + - - +
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Residues in contact with LEU1194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839F LEU* 4.9 7.2 - - + +
840F VAL 4.4 0.7 - - - -
841F GLY* 3.7 29.2 - - - +
842F PRO* 4.9 1.6 - - - +
1072F VAL* 3.4 23.6 - - - +
1073F ARG* 3.0 14.0 + - + +
1075F PHE* 3.7 25.5 - - + -
1099F GLU 4.5 0.9 - - - -
1100F MET* 4.8 5.8 - - + -
1193F SER* 1.3 72.6 - - - +
1195F GLY* 1.3 63.4 + - - +
1198F GLN 5.2 1.6 - - - +
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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