Contacts of the strand formed by residues 1099 - 1106 (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 GLN1099 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036B ARG* 3.0 43.7 + - - +
1037B PHE 3.2 4.0 - - - +
1038B ASN* 3.2 28.3 + - - +
1065B MET 3.7 0.7 - - - +
1066B LYS* 3.5 2.4 - - - -
1067B ASN* 2.7 44.4 + - - +
1097B GLY 3.8 10.3 + - - +
1098B ASP* 1.3 76.8 - - - +
1100B ILE* 1.3 63.2 + - - +
1101B TRP* 3.8 2.5 - - - -
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Residues in contact with ILE1100 (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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1035B GLY 4.1 0.5 - - - +
1036B ARG* 3.7 0.9 - - - -
1037B PHE* 2.9 51.4 + - + +
1047B PHE* 3.4 38.6 - - + -
1064B LEU* 3.6 25.4 - - + -
1065B MET 3.3 8.1 - - - +
1066B LYS* 3.8 24.2 - - + -
1071B LEU* 4.2 7.4 - - + -
1094B LEU* 3.7 25.6 - - + -
1098B ASP 5.2 0.2 - - - +
1099B GLN* 1.3 80.2 - - - +
1101B TRP* 1.3 66.6 + - - +
1119B PHE* 4.2 6.2 - - + -
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Residues in contact with TRP1101 (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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1014B ASP 5.3 2.7 - - - -
1016B PRO* 3.7 34.8 - - + -
1034B LEU 5.4 0.4 - - - +
1035B GLY 3.6 17.5 - - - +
1036B ARG* 3.4 43.8 - - + +
1064B LEU* 3.6 3.1 - - - +
1065B MET* 2.7 61.1 + - + +
1067B ASN 2.8 28.1 + - - -
1068B GLU* 5.4 1.1 - - - -
1099B GLN 3.8 11.4 - - - -
1100B ILE* 1.3 80.7 - - - +
1102B LEU* 1.3 84.3 + - - +
1103B ARG* 3.5 35.9 - - + -
1119B PHE* 4.3 6.7 - - - -
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Residues in contact with LEU1102 (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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1017B ILE* 2.8 47.2 + - + +
1019B PHE* 4.0 4.5 - - + -
1035B GLY 4.5 2.4 + - - -
1049B PHE* 3.8 30.3 - - + -
1051B MET* 3.6 33.9 - - + -
1062B VAL* 4.1 4.7 - - + -
1063B ASN 3.4 10.1 - - - +
1064B LEU* 3.7 27.4 - - + -
1101B TRP* 1.3 83.2 - - - +
1103B ARG* 1.3 60.4 + - - +
1119B PHE* 3.7 30.9 - - + -
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Residues in contact with ARG1103 (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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1114A TRP* 3.4 26.3 - - - -
1014B ASP* 3.4 49.4 + - - +
1015B GLN 3.6 3.1 - - - +
1017B ILE* 4.0 2.5 - - - -
1062B VAL* 3.4 5.5 - - - +
1063B ASN* 2.8 61.4 + - - +
1065B MET* 3.6 29.3 - - + +
1068B GLU 5.7 0.4 + - - -
1070B VAL* 3.9 8.3 - - - +
1101B TRP* 3.5 30.0 + - + -
1102B LEU* 1.3 72.8 - - - +
1104B LEU* 1.3 62.9 + - - +
1105B HIS* 3.2 4.2 + - - -
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Residues in contact with LEU1104 (chain B).
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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1008B LEU* 4.1 6.7 - - + +
1010B PRO* 3.6 32.5 - - + -
1012B THR 5.0 1.1 - - - +
1013B LEU* 4.0 0.7 - - - -
1014B ASP* 2.9 23.2 + - - -
1015B GLN* 2.8 17.9 + - - +
1016B PRO 5.4 0.2 - - - +
1017B ILE* 3.6 20.0 - - + +
1060B LEU* 3.4 22.0 - - + -
1061B TYR 3.7 2.7 - - - +
1062B VAL* 4.6 0.9 - - + +
1103B ARG* 1.3 69.4 - - - +
1105B HIS* 1.3 60.3 + - - +
1106B ARG 3.2 28.7 - - - +
1107B GLY 3.5 20.0 - - - +
1108B ALA* 4.1 7.9 - - - -
1109B ILE* 4.2 15.0 - - + -
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Residues in contact with HIS1105 (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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1114A TRP* 3.5 30.8 - + + -
1013B LEU* 3.3 22.9 - - + +
1014B ASP* 2.7 51.3 + - - +
1061B TYR* 2.9 37.3 + + + +
1063B ASN* 3.8 15.5 - - - +
1103B ARG* 3.2 4.8 + - - -
1104B LEU* 1.3 72.9 - - - +
1106B ARG* 1.3 84.1 + - + +
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Residues in contact with ARG1106 (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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1013B LEU* 3.8 39.7 - - + +
1058B VAL* 4.5 8.1 - - + -
1059B PRO* 3.6 27.4 - - - +
1060B LEU* 3.4 1.2 - - - -
1061B TYR* 2.9 38.0 + - + -
1104B LEU* 3.2 11.7 - - - +
1105B HIS* 1.3 103.4 + - + +
1107B GLY* 1.3 63.8 + - - +
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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