Contacts of the strand formed by residues 1113 - 1122 (chain A) in PDB entry 5J67
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 LEU1113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793A ARG* 3.5 31.6 - - - +
1056A LYS* 3.5 6.6 - - - +
1057A VAL* 2.9 57.8 + - + +
1112A GLY* 1.3 71.3 - - - -
1114A TYR* 1.3 62.8 + - - +
1134A THR* 4.5 4.5 - - + -
1135A LEU 3.5 30.5 - - - +
1136A ARG* 3.8 27.3 - - + +
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Residues in contact with TYR1114 (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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1054A HIS* 4.9 7.6 - + - -
1055A LYS 3.3 17.5 - - - +
1056A LYS* 3.6 25.8 - - + +
1057A VAL* 5.0 1.1 - - - -
1108A LEU* 3.7 26.9 - - + +
1109A GLU* 2.8 51.5 + - - +
1112A GLY* 3.5 20.0 - - - -
1113A LEU* 1.3 76.4 - - - +
1115A LYS* 1.3 61.1 + - - +
1116A PHE* 3.7 28.1 - + + -
1133A VAL 4.0 0.3 - - - +
1134A THR* 3.2 6.3 - - - -
1135A LEU* 2.8 35.4 + - + +
1137A THR* 3.8 18.4 - - + -
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Residues in contact with LYS1115 (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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1053A GLN 4.1 0.3 - - - +
1054A HIS* 3.3 3.8 - - - +
1055A LYS* 2.8 58.0 + - + +
1057A VAL* 4.2 15.0 - - + +
1114A TYR* 1.3 73.5 - - - +
1116A PHE* 1.3 63.0 + - - +
1117A THR* 3.9 16.5 - - + +
1132A THR* 3.7 26.2 + - + +
1133A VAL 3.4 2.7 - - - -
1134A THR* 3.5 24.1 - - + +
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Residues in contact with PHE1116 (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 LEU* 3.7 19.2 - - + +
1032A VAL* 4.3 11.9 - - + -
1034A LEU* 3.6 18.8 - - + -
1052A LEU* 4.9 2.9 - - + -
1053A GLN 3.4 4.7 - - - +
1054A HIS* 3.4 28.5 - + + -
1105A PHE* 3.5 29.6 - + - -
1108A LEU* 4.1 20.2 - - + -
1114A TYR* 3.7 28.9 - + + -
1115A LYS* 1.3 74.4 - - - +
1117A THR* 1.3 60.7 - - - +
1132A THR* 3.4 2.4 - - - +
1133A VAL* 2.7 49.0 + - + +
1135A LEU* 4.1 26.5 - - + -
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Residues in contact with THR1117 (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 LEU* 4.5 2.0 - - - -
1051A ILE 3.8 0.2 - - - +
1052A LEU* 3.3 6.2 - - - +
1053A GLN* 2.9 58.4 + - - +
1115A LYS* 3.9 17.5 - - + -
1116A PHE* 1.3 79.7 - - - +
1118A LEU* 1.3 62.4 + - - +
1119A TYR* 5.7 1.0 - - - -
1130A LEU* 3.8 23.8 - - + +
1131A SER 3.2 6.5 - - - -
1132A THR* 3.6 25.8 - - + +
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Residues in contact with LEU1118 (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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1017A PRO* 3.7 30.3 - - + +
1019A LEU* 4.1 20.4 - - + -
1036A TRP* 3.5 64.8 - - + -
1050A TYR* 4.1 11.0 - - + -
1051A ILE 3.4 15.0 - - - +
1052A LEU* 4.0 11.7 - - + -
1117A THR* 1.3 74.1 - - - +
1119A TYR* 1.3 65.8 + - - +
1129A GLU 4.3 0.5 - - - +
1130A LEU* 3.6 1.8 - - - -
1131A SER* 2.7 40.1 + - - +
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Residues in contact with TYR1119 (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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1017A PRO* 4.1 7.2 - - - -
1050A TYR* 3.5 4.1 - - - -
1051A ILE* 2.8 79.9 + - + +
1053A GLN* 4.2 17.7 + - + -
1070A PHE* 3.9 10.6 - - - -
1117A THR 5.7 0.4 - - - -
1118A LEU* 1.3 77.8 - - - +
1120A ALA* 1.3 69.0 + - - +
1121A VAL* 3.8 1.6 - - + -
1127A HIS* 3.4 48.7 + + + -
1128A SER* 3.4 20.9 - - - +
1130A LEU* 4.2 22.4 - - + -
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Residues in contact with ALA1120 (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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1014A LEU* 4.1 9.0 - - + -
1017A PRO* 3.9 4.2 - - + +
1039A VAL* 3.9 17.7 - - + -
1047A VAL* 4.2 4.7 - - + -
1049A ASP 3.5 4.9 - - - -
1050A TYR* 3.6 24.9 - - + -
1119A TYR* 1.3 75.2 - - - +
1121A VAL* 1.3 66.3 + - - +
1122A ASP 4.3 0.4 - - - -
1127A HIS* 3.5 2.8 - - - -
1128A SER* 2.8 43.1 + - - +
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Residues in contact with VAL1121 (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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1014A LEU* 4.8 0.2 - - - -
1047A VAL* 3.7 3.1 - - - +
1048A SER* 2.7 42.6 + - - +
1049A ASP* 2.7 23.5 + - + +
1051A ILE* 3.9 17.9 - - + -
1119A TYR* 3.8 23.1 - - + -
1120A ALA* 1.3 79.8 - - - +
1122A ASP* 1.3 62.3 + - - +
1125A GLY* 4.2 10.8 - - - +
1126A ARG 3.3 11.4 - - - +
1127A HIS* 3.8 14.4 - - + +
1260A TYR* 5.1 5.2 - - + -
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Residues in contact with ASP1122 (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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1009A PRO 4.6 1.9 - - - +
1014A LEU* 4.1 9.6 - - + +
1045A THR* 3.4 19.9 - - + +
1046A LYS 3.2 13.9 - - - +
1047A VAL* 4.1 1.8 - - - +
1048A SER* 3.1 14.1 + - - -
1121A VAL* 1.3 75.8 - - - +
1123A THR* 1.3 64.6 + - - +
1124A ARG* 3.2 9.9 + - - +
1125A GLY* 2.7 38.8 + - - -
1126A ARG* 2.7 59.3 + - - +
1260A TYR* 3.9 1.2 - - - -
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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