Contacts of the strand formed by residues 1180 - 1190 (chain A) in PDB entry 4UHW
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 HIS1180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A GLN* 3.6 18.4 + - - -
556A LEU* 4.0 5.6 - - - -
1171A VAL* 4.2 2.5 - - + -
1172A GLU 3.3 13.5 - - - +
1173A ILE* 3.9 15.3 - - + -
1178A GLY 5.3 0.4 + - - -
1179A ASP* 1.3 82.4 + - - +
1181A LYS* 1.3 74.0 + - - +
1182A ASN* 3.1 32.9 + - - -
1216A THR* 4.3 17.4 + - - +
1217A ILE* 4.9 10.8 - - + -
1243A ASP* 5.9 2.0 - - - -
1279A VAL* 4.2 3.0 - - - +
1283A ILE* 3.7 31.7 - - + +
1306A LEU 5.3 2.0 - - - -
1308A PRO* 6.1 2.6 - - - +
1311A ILE* 4.2 11.9 - - + +
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Residues in contact with LYS1181 (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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434A GLN* 4.5 13.5 + - - +
556A LEU* 3.8 25.6 - - + +
558A SER* 3.3 40.0 - - - +
561A HIS* 4.7 5.1 - - - -
1171A VAL* 3.2 6.6 - - - +
1172A GLU* 3.0 36.7 + - + +
1180A HIS* 1.3 76.7 - - - +
1182A ASN* 1.3 77.4 + - - +
1183A ILE* 3.5 8.3 + - + +
1242A CYS* 4.0 19.9 + - - +
1244A MET 4.7 6.9 + - - -
1246A THR* 3.1 25.4 + - - +
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Residues in contact with ASN1182 (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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1170A GLU 3.8 5.8 - - - +
1171A VAL* 3.4 2.6 - - - +
1180A HIS* 3.1 29.2 + - - -
1181A LYS* 1.3 83.4 - - - +
1183A ILE* 1.3 61.8 + - - +
1184A ARG 3.7 0.4 - - - +
1185A THR* 5.5 1.6 - - - +
1212A MET* 3.1 25.0 - - - +
1216A THR* 5.9 0.2 + - - -
1243A ASP* 3.0 26.7 + - - +
1244A MET 4.9 0.2 - - - -
1245A PRO* 3.5 20.9 - - + +
1246A THR 3.2 19.9 + - - -
1279A VAL* 3.2 22.0 - - + +
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Residues in contact with ILE1183 (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 LYS* 4.0 20.9 - - + +
1170A GLU* 2.8 39.2 + - + +
1171A VAL* 3.4 31.0 - - - +
1172A GLU* 3.5 15.9 - - + +
1181A LYS* 4.1 13.7 - - + +
1182A ASN* 1.3 74.3 - - - +
1184A ARG* 1.3 62.1 + - + +
1246A THR* 3.2 16.2 - - - +
1247A GLU* 3.0 25.9 + - - +
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Residues in contact with ARG1184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983A MET* 3.8 15.2 + - - +
984A SER 3.3 19.0 + - - -
985A SER* 5.2 2.2 + - - -
989A ARG* 3.5 34.1 + - - +
1169A SER* 3.4 1.0 - - - -
1170A GLU* 2.9 28.8 + - - +
1182A ASN* 3.7 1.0 - - - -
1183A ILE* 1.3 88.9 - - + +
1185A THR* 1.3 71.4 + - - +
1186A ASP* 3.3 32.5 + - - +
1245A PRO* 4.4 1.8 - - - -
1247A GLU* 3.4 35.7 + - + +
1249A HIS* 3.6 27.3 + - - -
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Residues in contact with THR1185 (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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1167A ALA* 5.2 0.4 - - + -
1168A CYS 3.2 7.6 - - - +
1169A SER* 2.6 22.8 + - - +
1182A ASN* 5.5 1.2 - - - +
1184A ARG* 1.3 74.7 + - - +
1186A ASP* 1.3 68.1 + - - +
1187A ILE* 3.9 19.3 - - + -
1208A PHE* 3.5 36.4 - - + -
1245A PRO* 4.0 18.3 - - - +
1247A GLU 3.1 6.1 + - - -
1248A LEU* 3.4 8.9 - - + +
1249A HIS* 3.0 25.1 + - - +
1278A SER* 4.8 0.9 - - - +
1279A VAL* 4.7 2.6 - - - +
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Residues in contact with ASP1186 (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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980A CYS* 3.6 5.4 - - - -
983A MET* 3.7 15.7 - - + +
984A SER* 3.5 26.3 - - - -
989A ARG* 3.2 25.1 + - - -
1167A ALA* 3.2 4.5 - - - -
1168A CYS* 2.8 36.4 + - + +
1184A ARG* 3.3 29.2 + - - +
1185A THR* 1.3 77.0 - - - +
1187A ILE* 1.3 62.2 + - - +
1249A HIS* 3.4 21.6 - - - +
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Residues in contact with ILE1187 (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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983A MET* 3.6 2.6 - - - +
1166A ALA 3.6 4.0 - - - +
1167A ALA* 4.1 8.5 - - + -
1185A THR* 3.9 14.6 - - + -
1186A ASP* 1.3 79.2 - - - +
1188A VAL* 1.3 65.9 + - - +
1189A MET* 3.7 30.5 - - + -
1204A ILE* 4.0 17.0 - - + -
1205A GLU* 5.9 0.4 - - - -
1208A PHE* 3.9 36.3 - - + -
1248A LEU* 4.6 4.9 - - + -
1249A HIS 2.9 13.4 + - - +
1250A ILE* 3.3 18.4 - - + -
1251A ALA 2.8 26.7 + - - +
1275A LEU* 3.9 11.0 - - + -
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Residues in contact with VAL1188 (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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976A CYS* 4.0 25.5 - - - +
979A GLU* 3.6 31.9 - - + +
980A CYS* 3.8 28.2 - - + +
983A MET* 3.8 18.4 - - + -
1165A GLY* 3.3 2.9 - - - -
1166A ALA 3.0 32.4 + - - +
1187A ILE* 1.3 77.5 - - - +
1189A MET* 1.3 67.0 + - - +
1251A ALA* 3.4 14.1 - - + +
1253A LEU* 4.4 12.1 - - + +
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Residues in contact with MET1189 (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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976A CYS* 4.3 0.7 - - - -
1012A LEU* 3.9 23.8 - - + -
1163A VAL* 4.3 10.3 - - + -
1164A TYR 3.7 8.5 - - - +
1165A GLY* 4.2 2.0 - - - -
1187A ILE* 3.7 6.3 - - + -
1188A VAL* 1.3 77.6 - - - +
1190A ASP* 1.3 63.9 + - - +
1191A VAL* 3.5 14.5 + - + +
1204A ILE* 3.6 50.7 - - + -
1251A ALA 3.0 12.8 + - - +
1252A LEU* 3.4 8.6 - - + -
1253A LEU* 3.1 22.1 + - - -
1268A LEU* 5.5 2.5 - - + -
1271A SER* 4.8 3.8 - - - -
1272A GLY* 4.6 8.3 - - - +
1275A LEU* 3.4 30.3 - - + -
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Residues in contact with ASP1190 (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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972A ASN* 2.8 36.8 + - + +
976A CYS* 3.8 9.6 - - - -
1163A VAL* 3.6 22.9 - - - +
1164A TYR* 2.8 31.2 + - + +
1189A MET* 1.3 69.0 - - - +
1191A VAL* 1.3 59.8 + - - +
1192A GLY* 3.1 18.7 + - - -
1253A LEU* 4.0 18.6 - - + +
1254A PRO 5.5 0.3 - - - +
1255A PRO* 5.6 2.1 - - - +
1256A SER 5.8 0.5 + - - -
1266A LYS* 3.0 28.5 + - - +
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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