Contacts of the strand formed by residues 1043 - 1052 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041B VAL 3.4 2.8 + - - -
1042B ASN* 1.3 75.8 - - - +
1044B THR* 1.3 58.3 + - - -
1045B TYR* 3.3 13.1 - - - -
1093B GLN* 3.5 3.8 - - - -
1094B LEU 2.8 33.6 + - - -
1123B LEU* 4.2 1.1 - - - -
1125B TYR 3.2 12.3 - - - -
1126B GLN* 4.2 0.7 - - - -
1127B ASP 3.5 15.3 + - - -
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Residues in contact with THR1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999A ALA* 4.5 10.3 - - + -
1024A ASN* 3.3 30.3 + - - +
1026A LEU* 3.7 17.8 - - + +
1043B GLY* 1.3 73.3 - - - -
1045B TYR* 1.3 56.7 + - - +
1091B ILE* 3.7 16.2 - - + -
1092B LEU 3.5 4.5 - - - +
1093B GLN* 4.3 5.8 - - - +
1123B LEU* 3.4 2.8 - - - +
1124B LEU* 2.8 34.0 + - + +
1125B TYR* 2.7 31.0 + - + +
1127B ASP 5.4 2.8 - - - -
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Residues in contact with TYR1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B VAL* 4.3 6.7 - - + -
1037B PHE* 3.6 26.9 - + - -
1039B CYS* 3.6 16.9 - - - -
1040B PRO* 3.7 5.9 - - - +
1041B VAL* 2.6 44.2 + - - +
1043B GLY 3.3 25.8 - - - -
1044B THR* 1.3 75.1 - - - +
1046B VAL* 1.3 64.3 + - - +
1047B PHE* 3.7 22.0 - + + -
1090B ALA 3.8 0.3 - - - +
1091B ILE* 3.2 5.6 - - - +
1092B LEU* 2.9 36.1 + - - +
1094B LEU* 3.8 14.6 - - + -
1122B TYR* 3.4 19.1 - - - +
1123B LEU* 3.4 26.6 - - + +
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Residues in contact with VAL1046 (chain B).
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* 6.4 1.8 - - + -
1122A TYR* 4.2 12.1 - - + -
1045B TYR* 1.3 74.8 - - - +
1047B PHE* 1.3 72.7 + - - +
1048B ILE* 4.4 13.0 - - + -
1089B HIS* 5.8 1.8 - - + -
1090B ALA 3.4 9.2 - - - +
1091B ILE* 3.9 28.5 - - + -
1121B GLY* 3.0 5.2 - - - -
1122B TYR* 3.0 74.1 + - + +
1124B LEU* 4.4 12.1 - - + -
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Residues in contact with PHE1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000B PHE* 4.0 17.3 - + - -
1037B PHE* 3.9 19.1 - + - -
1045B TYR* 3.7 18.2 - + + -
1046B VAL* 1.3 78.9 - - - +
1048B ILE* 1.3 67.8 + - - +
1049B PHE* 5.7 1.1 - - + -
1064B LEU* 4.2 16.2 - - + -
1089B HIS* 3.1 5.1 - - - +
1090B ALA 2.9 35.1 + - - +
1092B LEU* 3.4 37.7 - - + -
1094B LEU* 3.8 9.0 - - + -
1100B ILE* 3.4 41.7 - - + -
1119B PHE* 4.3 9.0 - + + -
1120B SER 3.3 7.4 - - - +
1121B GLY* 3.8 11.4 - - - -
1122B TYR 5.1 0.2 - - - -
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Residues in contact with ILE1048 (chain B).
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* 4.6 20.2 - - + -
1050A HIS* 5.4 0.2 - - + -
1046B VAL* 4.4 15.3 - - + -
1047B PHE* 1.3 80.8 - - - +
1049B PHE* 1.3 68.7 + - - +
1050B HIS* 3.8 14.8 - - + -
1087B SER* 5.2 0.4 - - - +
1088B ASN 3.6 11.4 - - - +
1089B HIS* 4.3 8.1 - - + -
1119B PHE* 3.5 1.5 - - - -
1120B SER* 2.9 34.2 + - - +
1122B TYR* 5.2 9.0 - - + +
1046C VAL* 5.3 10.3 - - + -
1048C ILE* 5.1 7.2 - - + -
1089C HIS* 3.5 39.1 - - + +
1091C ILE* 6.1 1.8 - - + -
1122C TYR* 6.0 0.7 - - - +
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Residues in contact with PHE1049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047B PHE 5.7 0.4 - - - -
1048B ILE* 1.3 79.7 - - - +
1050B HIS* 1.3 64.9 + - - +
1051B MET* 4.1 11.9 - - + -
1062B VAL* 3.7 28.7 - - + -
1064B LEU* 4.2 22.7 - - + -
1072B VAL* 4.4 2.2 - - + -
1073B SER 4.7 1.3 - - - -
1074B ALA* 3.7 26.7 - - + -
1086B ALA 4.0 9.2 - - - -
1087B SER* 3.0 28.9 + - - -
1088B ASN* 3.1 44.8 + - + -
1089B HIS* 5.3 0.7 - - - -
1102B LEU* 3.8 30.1 - - + -
1118B THR 3.2 13.0 - - - +
1119B PHE* 3.8 4.7 - + + -
1089C HIS* 3.9 2.2 - - - -
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Residues in contact with HIS1050 (chain B).
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* 5.1 1.2 + - - -
1048B ILE* 3.8 14.6 - - + -
1049B PHE* 1.3 72.0 - - - +
1051B MET* 1.3 62.2 + - - +
1052B LEU 4.2 0.4 - - - -
1085B THR* 4.2 10.3 - - + -
1086B ALA 3.6 3.8 - - - -
1087B SER* 3.3 27.8 + - - -
1116B TYR 4.2 4.0 - - - +
1117B SER* 3.1 3.6 - - - -
1118B THR* 2.7 43.3 + - - +
1048C ILE* 5.3 4.7 - - + -
1050C HIS* 4.9 3.0 + - - -
1087C SER* 3.0 43.1 + - - +
1088C ASN* 3.6 26.3 + - - +
1089C HIS* 2.9 33.0 + - + -
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Residues in contact with MET1051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B ARG* 6.2 0.2 - - - -
1017B ILE* 4.3 9.4 - - - -
1019B PHE* 3.8 13.7 - - + -
1049B PHE* 4.1 14.1 - - + -
1050B HIS* 1.3 78.8 - - - +
1052B LEU* 1.3 61.2 + - - +
1060B LEU* 3.7 19.1 - - + +
1062B VAL* 4.2 10.8 - - + -
1084B GLU 3.5 0.9 - - - +
1085B THR* 3.3 5.3 - - - +
1086B ALA 2.7 41.3 + - - +
1102B LEU* 3.6 21.8 - - + -
1109B ILE* 3.5 31.2 - - + -
1117B SER* 3.9 11.7 - - - -
1118B THR 3.2 38.1 - - - +
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Residues in contact with LEU1052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B HIS 4.2 0.8 - - - -
1051B MET* 1.3 70.9 - - - +
1053B LYS* 1.3 65.2 + - - +
1060B LEU* 4.4 1.1 - - - -
1083B HIS* 3.9 22.2 - - + +
1084B GLU* 3.4 18.2 - - - +
1085B THR* 3.5 22.7 - - + +
1109B ILE* 3.4 8.5 - - - +
1110B TYR* 2.8 45.2 + - + -
1116B TYR* 3.8 40.1 + - + +
1117B SER* 3.1 16.3 + - - +
1075C TYR* 4.3 21.5 - - + +
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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