Contacts of the strand formed by residues 1043 - 1052 (chain A) in PDB entry 4OUL
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 GLY1043 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041A VAL 3.3 3.2 + - - -
1042A ASN* 1.3 75.4 - - - +
1044A THR* 1.3 61.7 + - - -
1045A TYR* 3.2 13.3 - - - -
1093A GLN* 3.4 3.7 - - - -
1094A LEU 2.7 38.9 + - - -
1123A LEU* 4.3 0.2 - - - -
1125A TYR 3.1 12.1 - - - -
1126A GLN* 4.3 0.9 - - - -
1127A ASP* 3.8 9.1 - - - +
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Residues in contact with THR1044 (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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1043A GLY* 1.3 72.7 - - - -
1045A TYR* 1.3 57.1 + - - +
1091A ILE* 3.7 26.7 - - + -
1092A LEU 3.5 8.5 - - - +
1093A GLN* 4.4 5.9 - - - +
1123A LEU* 3.2 7.8 - - - +
1124A LEU* 2.7 40.4 + - + -
1125A TYR* 2.7 27.0 + - + +
999C ALA* 4.5 4.3 - - + -
1024C ASN* 3.8 15.8 + - - +
1026C LEU* 3.6 19.8 - - + +
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Residues in contact with TYR1045 (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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998A VAL* 3.5 17.8 - - + +
1037A PHE* 3.3 30.7 - + - -
1039A CYS* 3.7 13.0 - - - -
1040A PRO* 3.4 5.0 - - - +
1041A VAL* 2.5 50.6 + - - +
1043A GLY 3.2 24.9 - - - -
1044A THR* 1.3 74.0 - - - +
1046A VAL* 1.3 63.1 + - - +
1047A PHE* 3.6 22.4 - + + -
1090A ALA 3.8 0.9 - - - +
1091A ILE* 3.2 5.0 - - - +
1092A LEU* 2.9 35.0 + - - +
1094A LEU* 3.7 14.4 - - + -
1122A TYR* 3.4 10.3 - - - +
1123A LEU* 3.7 21.9 - - + +
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Residues in contact with VAL1046 (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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1045A TYR* 1.3 73.0 - - - +
1047A PHE* 1.3 73.6 + - - +
1048A ILE* 5.7 4.3 - - + -
1089A HIS* 5.8 3.1 - - + -
1090A ALA 3.4 7.0 - - - +
1091A ILE* 3.9 17.5 - - + -
1121A GLY* 3.0 5.2 - - - -
1122A TYR* 2.9 58.4 + - + +
1124A LEU* 3.7 37.2 - - + -
1048C ILE* 6.4 2.0 - - + -
1122C TYR* 4.1 16.4 - - + +
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Residues in contact with PHE1047 (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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1000A PHE* 3.9 18.2 - + - -
1037A PHE* 3.7 26.9 - + - -
1045A TYR* 3.6 26.5 - + + -
1046A VAL* 1.3 79.9 - - - +
1048A ILE* 1.3 62.9 + - - +
1049A PHE* 5.8 1.3 - - + -
1064A LEU* 4.1 17.0 - - + -
1089A HIS* 3.1 7.3 - - - +
1090A ALA 2.8 35.7 + - - +
1092A LEU* 3.8 27.6 - - + -
1094A LEU* 4.0 0.4 - - + -
1100A ILE* 3.5 42.0 - - + -
1119A PHE* 4.2 7.0 - + + -
1120A SER 3.4 6.3 - - - +
1121A GLY* 3.8 12.3 - - - -
1122A TYR 5.2 0.2 - - - -
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Residues in contact with ILE1048 (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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1046A VAL* 5.7 4.7 - - + -
1047A PHE* 1.3 77.5 - - - +
1049A PHE* 1.3 69.6 + - - +
1050A HIS* 3.7 28.7 - - + -
1087A SER* 5.1 0.7 - - - +
1088A ASN 3.5 12.8 - - - +
1089A HIS* 4.2 4.3 - - + +
1119A PHE* 3.5 2.2 - - - -
1120A SER* 3.0 37.1 + - - +
1122A TYR* 6.2 2.9 - - + -
1046B VAL* 6.4 1.6 - - + -
1048B ILE* 4.6 15.0 - - + -
1050B HIS* 6.3 0.4 - - + -
1089B HIS* 3.4 35.9 - - + +
1091B ILE* 5.6 2.5 - - + -
1048C ILE* 3.9 24.7 - - + -
1050C HIS* 5.3 1.1 - - + -
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Residues in contact with PHE1049 (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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1047A PHE 5.8 0.2 - - - -
1048A ILE* 1.3 79.8 - - - +
1050A HIS* 1.3 61.0 + - - +
1051A MET* 4.2 7.4 - - + -
1062A VAL* 3.7 31.2 - - + -
1064A LEU* 4.1 22.7 - - + -
1072A VAL* 4.4 3.1 - - + -
1073A SER 4.6 0.9 - - - -
1074A ALA* 3.7 27.4 - - + -
1086A ALA 3.9 9.6 - - - -
1087A SER* 2.8 34.7 + - - -
1088A ASN* 3.0 46.7 + - + -
1089A HIS* 5.3 0.7 - - - -
1102A LEU* 3.7 32.3 - - + -
1118A THR 3.3 13.0 - - - +
1119A PHE* 4.0 3.8 - + + -
1089B HIS* 4.1 1.6 - - - -
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Residues in contact with HIS1050 (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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1048A ILE* 3.7 22.2 - - + -
1049A PHE* 1.3 71.5 - - - +
1051A MET* 1.3 63.2 + - - +
1052A LEU 4.2 0.2 - - - -
1085A THR* 4.4 9.9 - - + -
1086A ALA 3.6 3.8 - - - -
1087A SER* 3.1 29.4 + - - -
1116A TYR 4.1 6.5 - - - +
1117A SER* 3.1 3.7 - - - -
1118A THR* 2.7 44.2 + - - +
1048B ILE* 5.4 1.3 - - + -
1050B HIS* 5.1 1.4 + - - -
1087B SER* 3.0 39.7 + - - +
1088B ASN* 3.5 23.0 + - - +
1089B HIS* 3.0 30.1 + - + -
1050C HIS* 4.9 2.4 + - - -
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Residues in contact with MET1051 (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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1004A ARG* 5.9 0.2 - - - -
1017A ILE* 4.3 8.5 - - - -
1019A PHE* 3.8 14.6 - - + -
1049A PHE* 4.2 10.5 - - + -
1050A HIS* 1.3 79.0 - - - +
1052A LEU* 1.3 61.1 + - - +
1053A LYS 3.7 0.7 + - - -
1060A LEU* 3.9 16.7 - - + +
1062A VAL* 4.1 22.2 - - + -
1084A GLU 3.7 0.9 - - - +
1085A THR* 3.4 5.0 - - - +
1086A ALA* 2.8 42.9 + - - +
1102A LEU* 3.7 18.4 - - + -
1109A ILE* 3.6 26.2 - - + -
1117A SER* 3.8 12.6 - - - -
1118A THR 3.2 38.1 - - - +
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Residues in contact with LEU1052 (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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1050A HIS 4.2 0.6 - - - -
1051A MET* 1.3 72.3 - - - +
1053A LYS* 1.3 64.1 + - - +
1060A LEU* 4.4 1.1 - - - -
1083A HIS* 4.0 23.1 - - + -
1084A GLU 3.4 11.7 - - - +
1085A THR* 3.4 24.2 - - + +
1109A ILE* 3.5 5.2 - - - -
1110A TYR* 2.8 48.9 + - + -
1116A TYR* 3.8 44.7 + - + +
1117A SER* 3.1 11.1 + - - +
1075B TYR* 4.1 22.9 - - + +
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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