Contacts of the strand formed by residues 1098 - 1104 (chain B) in PDB entry 3E0D
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 PRO1098 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015B VAL* 6.3 1.8 - - + -
1018B TYR* 5.5 4.9 - - + +
1021B LEU* 4.7 13.7 - - + -
1049B GLY 3.4 13.5 - - - +
1050B MET* 3.6 20.4 - - + -
1096B ASP 4.3 2.7 - - - +
1097B ILE* 1.3 94.2 - - + +
1099B LEU* 1.3 70.6 + - - +
1121B LEU* 3.8 45.5 + - + -
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Residues in contact with LEU1099 (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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1021B LEU* 5.9 3.6 - - - -
1047B LEU 4.0 0.2 - - - +
1048B SER* 3.3 5.6 - - - -
1049B GLY 3.2 31.5 + - - +
1051B VAL* 3.6 29.4 - - + +
1068B PHE* 4.7 9.4 - - + -
1070B LEU* 4.3 4.2 - - + +
1097B ILE* 3.8 7.1 + - + +
1098B PRO* 1.3 82.1 - - - +
1100B LEU* 1.3 63.8 + - - +
1101B VAL* 4.3 5.8 - - + -
1118B VAL* 3.6 33.0 - - + -
1119B TRP 3.4 20.9 - - - +
1120B THR* 3.9 15.5 - - + -
1121B LEU 5.3 0.4 - - - +
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Residues in contact with LEU1100 (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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1021B LEU* 5.0 5.5 - - + +
1024B VAL* 3.8 26.2 - - + -
1025B ALA* 4.8 4.9 - - - +
1046B LEU* 4.1 27.4 - - + -
1047B LEU 3.6 11.7 - - - +
1048B SER* 3.7 22.4 - - - +
1099B LEU* 1.3 74.3 - - - +
1101B VAL* 1.3 64.9 + - - +
1118B VAL* 3.5 2.4 - - - +
1119B TRP* 3.1 54.7 + - + +
1120B THR 5.5 0.2 - - - -
1124B VAL* 4.0 30.7 - - + +
1205B PHE* 6.5 0.9 - - + -
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Residues in contact with VAL1101 (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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1045B VAL 3.5 1.6 - - - +
1046B LEU* 3.0 8.2 - - - -
1047B LEU* 2.7 47.4 + - + +
1068B PHE* 4.1 15.5 - - + -
1070B LEU* 4.4 15.7 - - + -
1079B VAL* 4.5 8.3 - - + -
1099B LEU* 4.3 12.3 - - + -
1100B LEU* 1.3 81.2 - - - +
1102B LEU* 1.3 69.7 + - - +
1103B ALA* 4.0 8.3 + - + +
1113B VAL* 6.0 0.2 - - + -
1115B ALA* 4.0 20.2 - - + -
1117B ALA 3.6 10.3 - - - +
1118B VAL* 3.8 13.9 - - + -
1119B TRP* 4.6 1.6 - - - -
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Residues in contact with LEU1102 (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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1044B LYS* 5.2 6.3 - - + -
1045B VAL* 3.5 26.5 - - - +
1046B LEU* 3.8 21.1 - - + -
1101B VAL* 1.3 69.1 - - - +
1103B ALA* 1.3 55.8 + - - +
1115B ALA* 3.8 0.7 - - - -
1116B GLN* 2.8 34.4 + - + -
1117B ALA* 2.9 25.8 + - + +
1119B TRP* 3.6 33.9 - - + -
1205B PHE 6.1 1.1 - - - +
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Residues in contact with ALA1103 (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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1044B LYS* 3.3 4.9 - - - +
1045B VAL* 2.8 45.1 + - + +
1047B LEU* 5.7 4.5 - - + -
1101B VAL* 4.2 9.6 - - + +
1102B LEU* 1.3 76.6 - - - +
1104B GLU* 1.3 60.5 + - - +
1105B VAL* 4.1 1.9 + - + +
1113B VAL* 3.5 25.8 - - + -
1114B LEU 3.2 14.1 - - - +
1115B ALA* 3.6 8.7 - - - -
1116B GLN* 4.1 4.0 - - - +
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Residues in contact with GLU1104 (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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1042B LYS* 3.5 36.4 - - - +
1043B PRO 3.4 9.6 - - - +
1044B LYS* 3.6 20.5 - - + -
1103B ALA* 1.3 72.8 - - - +
1105B VAL* 1.3 64.5 + - - +
1106B GLU* 4.5 8.0 - - - +
1112B ARG 4.0 0.3 - - - +
1113B VAL* 3.4 4.3 - - - -
1114B LEU* 2.8 52.7 + - + +
1116B GLN* 3.5 25.4 + - - +
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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