Contacts of the strand formed by residues 1076 - 1082 (chain E) in PDB entry 3DLS
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 PHE1076 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986E GLU* 3.9 34.3 - - + -
989E ALA* 3.6 25.1 - - + +
990E ALA* 3.7 29.6 - - + -
1012E PHE* 4.3 13.2 - + - -
1029E PHE* 3.9 18.6 - - + -
1030E ILE 3.3 4.9 - - - -
1031E LYS* 3.7 45.3 - - + -
1032E LYS* 3.4 14.2 - - - +
1072E GLU* 3.7 0.7 - - - -
1073E ASN* 2.8 41.4 + - - +
1075E GLY* 1.3 82.4 - - - +
1077E PHE* 1.3 59.0 + - - +
1078E GLN* 3.5 12.0 - - - +
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Residues in contact with PHE1077 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029E PHE* 3.5 5.2 - - - -
1030E ILE* 2.7 51.2 + - + +
1032E LYS* 3.7 27.4 - - + -
1040E TRP* 3.8 21.1 - + - -
1048E LYS 3.4 23.8 - - - -
1049E VAL* 3.7 25.4 - - + -
1050E THR* 4.3 2.2 - - + -
1053E ILE* 3.5 29.6 - - + -
1070E ILE* 4.9 6.3 - - + -
1071E PHE 3.6 15.3 - - - -
1072E GLU* 3.6 21.3 - - + -
1076E PHE* 1.3 75.7 - - - +
1078E GLN* 1.3 67.0 + - - +
1079E LEU 4.1 0.2 - - - -
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Residues in contact with GLN1078 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990E ALA 3.0 28.9 - - - +
992E GLU 4.5 3.8 + - - -
995E TYR* 3.6 33.7 - - + +
1027E VAL* 4.2 4.9 - - + -
1028E LYS 3.6 3.8 - - - -
1029E PHE* 3.7 13.2 - - + -
1069E ASP 3.8 0.5 - - - +
1070E ILE* 3.3 7.4 - - - -
1071E PHE* 3.0 63.8 + - + +
1072E GLU* 3.9 3.6 - - - +
1073E ASN* 3.3 21.8 + - - +
1076E PHE* 3.5 15.2 - - - +
1077E PHE* 1.3 76.8 - - - +
1079E LEU* 1.3 60.9 + - - +
1080E VAL* 3.7 3.9 + - + +
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Residues in contact with LEU1079 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026E VAL 3.6 1.4 - - - +
1027E VAL* 3.4 2.8 - - - -
1028E LYS* 2.8 49.9 + - + +
1030E ILE* 4.3 13.0 - - + -
1052E GLU* 4.0 26.9 - - + +
1053E ILE* 4.3 22.2 - - + +
1056E LEU* 3.9 22.2 - - + -
1067E VAL* 3.9 35.0 - - + -
1069E ASP 4.2 0.7 - - - -
1070E ILE* 4.6 8.7 - - + -
1077E PHE* 4.1 1.0 - - - +
1078E GLN* 1.3 70.9 - - - +
1080E VAL* 1.3 65.1 + - - +
1081E MET* 4.0 17.2 + - + +
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Residues in contact with VAL1080 (chain E).
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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995E TYR* 4.2 20.9 - - + -
999E TYR* 3.8 40.2 - - + +
1025E VAL* 3.9 25.1 - - + -
1026E VAL 3.4 4.0 - - - +
1027E VAL* 4.4 4.5 - - + -
1067E VAL* 3.4 7.6 - - - +
1068E LEU* 2.7 35.2 + - + -
1069E ASP* 2.8 28.9 + - + +
1071E PHE* 4.2 4.7 - - + -
1078E GLN 4.2 6.7 - - - +
1079E LEU* 1.3 76.7 - - - +
1081E MET* 1.3 57.2 + - - +
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Residues in contact with MET1081 (chain E).
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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5E ADP 3.9 18.2 - - + +
1013E VAL* 5.4 0.2 - - + -
1025E VAL* 3.6 10.2 - - - +
1026E VAL* 2.8 54.3 + - + +
1028E LYS* 4.1 31.6 - - + -
1052E GLU* 5.7 1.1 - - - +
1056E LEU* 4.2 12.8 - - + -
1065E ILE* 3.8 27.4 - - + -
1066E LYS 3.2 12.1 - - - +
1067E VAL* 4.6 2.5 - - - -
1068E LEU* 3.7 5.3 - - - +
1079E LEU* 4.2 19.7 - - + +
1080E VAL* 1.3 77.9 - - - +
1082E GLU* 1.3 70.7 + - - +
1145E ILE* 5.4 2.5 - - - -
1146E ASP 5.8 2.5 - - - -
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Residues in contact with GLU1082 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ADP 3.1 24.8 + - - -
1025E VAL* 5.4 0.2 - - - -
1026E VAL* 4.2 1.0 - - - +
1064E ILE 4.2 1.4 - - - +
1065E ILE* 3.6 13.5 - - + -
1066E LYS* 2.8 53.8 + - + +
1068E LEU* 3.9 18.6 - - + +
1081E MET* 1.3 73.2 - - - +
1083E LYS* 1.3 60.3 + - - +
1084E HIS* 3.4 20.8 + - - +
1143E LYS* 3.5 23.7 - - - -
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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