Contacts of the strand formed by residues 1090 - 1097 (chain D) in PDB entry 5GLJ
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 GLU1090 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1149B SER* 3.2 21.5 - - - +
1150B VAL* 4.9 5.8 - - + -
1151B SER* 4.0 1.3 - - - +
1088D GLU 5.0 2.8 - - - +
1089D ARG* 1.3 80.7 - - - +
1091D ILE* 1.3 70.0 + - - +
1092D THR* 4.7 4.3 + - - +
1176D SER* 3.3 4.3 - - - -
1177D GLN* 2.9 36.3 + - + +
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Residues in contact with ILE1091 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145B ILE* 3.8 13.0 - - + -
1146B SER* 3.3 37.7 - - - +
1149B SER* 2.9 28.2 + - - +
1151B SER* 4.1 12.6 - - - +
1153B GLU* 4.7 0.4 - - - +
1174B VAL* 4.2 11.9 - - + -
1090D GLU* 1.3 74.7 - - - +
1092D THR* 1.3 71.3 + - - +
1093D LEU* 4.4 4.0 - - + -
1145D ILE* 3.8 15.0 - - + -
1174D VAL* 3.6 22.0 - - + -
1175D ILE 3.3 8.1 - - - +
1176D SER* 3.6 27.1 - - - -
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Residues in contact with THR1092 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090D GLU* 4.1 6.1 + - - +
1091D ILE* 1.3 77.8 + - - +
1093D LEU* 1.3 78.0 + - - +
1094D VAL* 4.0 1.8 - - + -
1137D CYS* 3.7 27.8 - - - -
1173D LEU 3.4 2.1 - - - +
1174D VAL* 3.6 2.6 - - - -
1175D ILE* 2.9 42.4 + - - +
1177D GLN* 3.0 23.3 + - - +
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Residues in contact with LEU1093 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093B LEU* 3.9 36.3 - - + -
1174B VAL* 4.9 2.9 - - + -
1091D ILE* 4.4 7.9 - - + -
1092D THR* 1.3 86.5 - - - +
1094D VAL* 1.3 60.7 + - - +
1095D ASN* 4.1 10.8 + - - +
1172D THR* 3.9 23.6 - - + -
1173D LEU 3.4 2.7 - - - -
1174D VAL* 3.8 27.4 - - + -
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Residues in contact with VAL1094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092D THR* 4.2 1.1 - - + -
1093D LEU* 1.3 75.6 - - - +
1095D ASN* 1.3 64.1 + - - +
1096D LEU* 3.7 26.1 + - + -
1135D ASP* 3.7 21.3 - - - +
1137D CYS* 3.8 23.3 - - + -
1138D LEU* 4.7 10.1 - - + +
1171D VAL 3.5 2.1 - - - +
1172D THR* 3.3 1.6 - - - -
1173D LEU* 2.8 51.8 + - + +
1175D ILE* 3.7 31.6 - - + -
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Residues in contact with ASN1095 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093D LEU* 4.1 10.6 + - - +
1094D VAL* 1.3 72.1 - - - +
1096D LEU* 1.3 69.4 + - - +
1135D ASP* 3.9 11.1 + - - +
1171D VAL 3.5 3.8 - - - +
1172D THR* 2.6 34.2 + - - +
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Residues in contact with LEU1096 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094D VAL* 3.7 17.0 - - + +
1095D ASN* 1.3 84.0 - - - +
1097D LYS* 1.3 67.0 + - - +
1098D LYS 4.3 0.2 - - - -
1104D LEU* 3.8 28.9 - - + +
1106D PHE* 4.4 2.9 - - + -
1131D PRO* 3.7 16.6 - - + +
1132D ALA* 4.0 24.7 - - + -
1135D ASP* 3.6 28.0 - - + -
1138D LEU* 5.0 0.7 - - + -
1169D GLU 3.7 0.2 - - - +
1170D ASP* 3.7 1.2 - - - +
1171D VAL* 2.8 34.7 + - + +
1173D LEU* 4.0 24.5 - - + -
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Residues in contact with LYS1097 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096D LEU* 1.3 78.7 - - - +
1098D LYS* 1.3 68.2 + - - +
1099D ASP* 4.4 0.5 - - - +
1104D LEU* 4.4 3.1 - - - -
1131D PRO* 3.4 23.8 - - - +
1169D GLU* 2.6 39.1 + - - +
1170D ASP* 3.2 26.7 - - + +
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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