Contacts of the strand formed by residues 1091 - 1099 (chain D) in PDB entry 1IV4
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 LEU1091 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1048D LEU* 4.1 17.0 - - + -
1081D MET* 5.5 7.0 - - + -
1084D VAL* 6.2 0.9 - - + -
1085D GLU* 6.0 1.8 - - - +
1089D ALA* 3.9 3.4 + - - +
1090D LYS* 1.3 73.1 - - - +
1092D LEU* 1.3 60.1 + - - +
1093D GLN 3.7 15.7 - - - +
1120D MET* 3.6 51.1 - - + +
1122D LEU* 3.5 24.8 - - + +
1148D VAL* 4.2 7.2 - - + -
1149D LEU 3.5 16.6 - - - +
1150D LEU* 3.9 24.9 - - + +
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Residues in contact with LEU1092 (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 LYS 3.3 4.9 + - - +
1091D LEU* 1.3 73.6 - - - +
1093D GLN* 1.3 62.5 + - + +
1122D LEU* 3.6 9.4 - - - +
1126D ARG* 3.1 60.9 - - - +
1149D LEU* 2.9 40.9 + - + +
1150D LEU* 4.5 1.3 - - - -
1151D ASP 4.3 21.1 - - - +
1202E ARG 5.7 1.1 - - - +
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Residues in contact with GLN1093 (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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1091D LEU* 3.7 7.5 - - - +
1092D LEU* 1.3 83.1 - - - +
1094D ALA* 1.3 70.6 + - - +
1095D SER* 5.3 0.7 - - - -
1122D LEU* 3.9 6.0 - - - +
1125D ASP 4.1 3.6 - - - +
1126D ARG* 3.1 45.8 - - - +
1128D GLY 5.5 0.2 - - - +
1148D VAL* 3.4 4.3 - - - -
1149D LEU* 3.0 36.1 + - + +
1202E ARG* 3.2 4.3 + - - +
1203E ILE* 2.9 46.0 - - + +
1250E SER 4.2 2.9 - - - +
1251E ALA* 2.9 27.0 - - - +
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Residues in contact with ALA1094 (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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1044D LEU* 3.9 15.9 - - + -
1093D GLN* 1.3 77.9 - - - +
1095D SER* 1.3 53.7 + - - +
1096D LEU* 4.3 4.5 - - + +
1116D LEU* 6.2 0.4 - - + -
1120D MET* 3.8 37.2 - - + -
1122D LEU* 3.9 3.1 - - + +
1126D ARG 3.0 9.6 + - - +
1127D ILE* 3.6 5.3 - - + +
1128D GLY 2.8 30.3 + - - +
1147D VAL 3.5 5.2 - - - -
1148D VAL* 4.2 2.5 - - + -
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Residues in contact with SER1095 (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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1044D LEU* 5.4 0.2 - - - +
1093D GLN* 4.8 1.5 - - - +
1094D ALA* 1.3 74.3 - - - +
1096D LEU* 1.3 61.2 + - - +
1128D GLY* 3.3 6.1 - - - -
1146D ALA* 3.5 1.0 - - - -
1147D VAL* 2.8 40.1 + - - -
1203E ILE* 4.2 10.3 - - - +
1204E GLY* 4.0 9.6 - - - -
1205E TYR* 3.0 34.1 + - - +
1250E SER* 2.7 25.8 + - - -
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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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1040D ALA* 3.9 20.6 - - + +
1044D LEU* 4.3 22.4 - - + -
1094D ALA* 4.7 4.9 - - + +
1095D SER* 1.3 78.6 + - - +
1097D VAL* 1.3 64.5 + - - +
1098D LEU* 3.8 25.6 - - + -
1116D LEU* 3.8 19.7 - - + -
1127D ILE* 5.3 0.2 - - + -
1128D GLY 2.8 17.9 + - - +
1129D LEU* 3.7 23.3 - - + +
1130D THR* 3.1 24.6 + - - +
1144D ALA* 5.0 2.5 - - + -
1145D ARG 3.2 14.1 - - - +
1146D ALA* 3.8 11.9 - - + -
1205E TYR* 4.8 0.9 - - - -
1250E SER* 4.9 0.3 + - - -
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Residues in contact with VAL1097 (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 76.0 - - - +
1098D LEU* 1.3 71.1 + - - +
1099D THR* 4.1 2.2 + - - +
1130D THR* 3.3 24.2 - - - +
1132D LYS* 4.0 26.7 - - + -
1143D GLN 3.9 0.3 - - - +
1144D ALA* 3.3 4.5 - - - -
1145D ARG 2.9 29.8 + - - +
1205E TYR* 3.6 33.0 - - + +
1206E GLY* 3.9 10.8 - - - -
1207E GLU* 3.8 28.7 - - + +
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Residues in contact with LEU1098 (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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1020D LEU* 4.4 17.7 - - + -
1021D CYS* 4.3 15.5 - - - -
1039D ALA* 5.7 0.4 - - + -
1040D ALA* 3.7 17.3 - - + +
1096D LEU* 3.8 8.1 - - + -
1097D VAL* 1.3 76.3 - - - +
1099D THR* 1.3 60.7 + - - +
1100D LEU* 4.1 11.6 + - + +
1105D LEU* 4.1 18.2 - - + -
1112D LEU* 5.4 1.1 - - + -
1129D LEU* 3.8 25.6 - - + -
1130D THR 3.0 10.1 + - - +
1131D PHE* 3.4 12.3 - - + +
1132D LYS 2.9 25.8 + - - +
1142D VAL* 5.3 3.6 - - + -
1143D GLN 3.4 3.6 - - - +
1144D ALA* 3.6 27.8 - - + -
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Residues in contact with THR1099 (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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1097D VAL* 4.1 6.1 + - - +
1098D LEU* 1.3 72.5 - - - +
1100D LEU* 1.3 67.2 + - - +
1132D LYS* 3.2 7.1 - - + +
1133D THR 3.7 21.3 - - - +
1134D SER* 3.9 15.5 - - - -
1141D HIS 3.8 1.9 - - - +
1142D VAL* 3.5 2.6 - - - +
1143D GLN* 2.8 60.1 + - - +
1145D ARG* 4.5 3.8 + - - +
1207E GLU* 3.7 19.4 + - - -
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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