Contacts of the strand formed by residues 1148 - 1155 (chain A) in PDB entry 5ID6
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 ASP1148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A GLU* 4.9 2.3 - - - +
836A ARG* 3.5 39.0 - - + +
1138A ARG* 2.4 51.5 + - - +
1139A ASN 3.4 5.0 - - - +
1140A SER* 3.3 15.9 + - - -
1145A THR 5.0 0.8 + - - +
1146A ASP 4.1 1.2 + - - -
1147A VAL* 1.3 73.5 - - - +
1149A PHE* 1.3 59.8 + - - +
1178A ASN* 3.7 12.0 - - + +
1179A ALA* 3.3 21.8 + - - +
1180A ASP* 4.3 5.7 + - - +
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Residues in contact with PHE1149 (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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1070A ASN* 4.4 9.0 - - - -
1071A ARG* 4.9 0.2 - - - -
1072A ILE* 3.4 29.8 - - + -
1137A MSE 3.4 1.4 - - - +
1138A ARG* 3.5 5.2 - - - +
1139A ASN* 3.0 59.6 + - + -
1141A ILE* 5.3 2.7 - - + -
1147A VAL* 3.4 32.8 - - + -
1148A ASP* 1.3 76.8 - - - +
1150A LEU* 1.3 68.0 + - - +
1151A ILE* 4.1 15.3 - - + -
1163A ASP* 4.1 4.5 - - - -
1164A SER* 3.8 11.0 - - - -
1165A ARG* 3.2 52.9 - - + -
1178A ASN* 5.1 0.2 - - - +
1179A ALA* 5.0 0.2 - - - -
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Residues in contact with LEU1150 (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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1002A SER 4.0 7.4 - - - +
1003A LYS* 5.3 1.1 - - - -
1004A ILE 4.4 0.7 - - - +
1137A MSE 3.2 41.5 - - + +
1138A ARG* 3.8 21.5 - - + -
1149A PHE* 1.3 76.9 - - - +
1151A ILE* 1.3 60.7 + - - +
1162A TYR* 3.6 24.2 - - + +
1163A ASP* 3.3 3.6 - - - -
1164A SER* 2.8 37.5 + - - +
1178A ASN 4.4 0.9 - - - +
1179A ALA* 4.1 13.0 - - + -
1182A ASN* 3.4 44.2 - - + +
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Residues in contact with ILE1151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1068A TYR* 3.6 6.7 - - + +
1069A GLY* 3.5 24.2 - - - -
1070A ASN 4.0 6.3 - - - +
1071A ARG* 3.3 48.7 + - - +
1137A MSE 3.0 31.0 + - - +
1139A ASN* 4.0 9.4 - - - +
1149A PHE* 4.1 8.0 - - + -
1150A LEU* 1.3 75.2 - - - +
1152A SER* 1.3 63.0 + - - +
1153A PRO* 4.1 1.2 - - - +
1161A PHE* 4.4 9.4 - - + -
1162A TYR* 3.2 12.1 - - - +
1163A ASP* 3.9 24.0 - - + +
1165A ARG* 4.4 2.0 - - - +
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Residues in contact with SER1152 (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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1005A ASP* 2.7 45.9 + - - +
1010A PHE* 4.9 0.9 - - - +
1071A ARG* 4.4 1.8 - - - -
1137A MSE 4.1 7.6 - - - -
1151A ILE* 1.3 75.4 - - - +
1153A PRO* 1.3 64.9 - - - +
1154A VAL* 3.0 16.1 + - - +
1161A PHE* 2.8 36.3 - - - -
1162A TYR* 3.1 16.8 + - - -
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Residues in contact with PRO1153 (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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1010A PHE* 3.9 26.0 - - + -
1064A LYS 3.7 0.3 - - - +
1065A LEU* 3.3 10.6 - - + -
1066A TYR* 2.7 42.4 + - - +
1071A ARG* 4.1 4.7 - - - +
1134A MSE 3.5 33.0 - - + +
1135A LEU* 4.4 9.2 - - + -
1137A MSE 4.0 15.7 - - + -
1151A ILE 4.1 0.9 - - - +
1152A SER* 1.3 85.3 - - - +
1154A VAL* 1.3 59.1 + - + +
1161A PHE* 3.4 14.7 - - + -
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Residues in contact with VAL1154 (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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1005A ASP* 3.9 5.4 - - - +
1007A SER* 5.5 0.2 + - - -
1008A THR* 4.2 3.9 - - + +
1010A PHE* 3.9 23.6 - - + -
1063A TRP* 3.4 31.4 - - + -
1064A LYS 3.6 19.5 - - - +
1065A LEU* 3.7 22.0 - - + -
1152A SER* 3.0 14.9 + - - +
1153A PRO* 1.3 86.3 - - + +
1155A LYS* 1.3 79.7 + - - +
1161A PHE* 2.9 19.8 - - - +
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Residues in contact with LYS1155 (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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1008A THR* 3.8 4.9 - - - +
1063A TRP* 5.5 0.2 - - - -
1064A LYS* 4.6 11.6 + - - +
1066A TYR* 3.9 28.8 - - + +
1068A TYR* 4.1 7.6 - - + +
1154A VAL* 1.3 90.4 - - - +
1156A ASN* 1.3 77.3 + - - +
1157A SER* 5.4 2.4 - - - +
1159A GLY* 3.4 29.2 - - - +
1160A ILE 4.1 0.2 - - - -
1161A PHE* 3.4 11.6 - - + -
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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