Contacts of the strand formed by residues 1025 - 1034 (chain B) in PDB entry 3LW0
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 GLU1025 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020B GLY* 4.3 9.5 + - - -
1022B VAL* 3.1 34.9 + - - +
1023B LYS 3.9 6.9 - - - +
1024B ASP* 1.3 81.8 - - - +
1026B PRO* 1.3 69.5 - - - +
1027B GLU* 3.1 11.0 + - - +
1028B THR* 2.7 43.3 + - - +
1084C ARG* 3.6 27.8 + - - +
1145C GLU* 4.7 2.9 - - - +
1146C ASP* 6.1 0.2 - - - -
1147C PHE* 4.3 9.3 - - + -
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Residues in contact with PRO1026 (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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1019B LYS* 3.5 8.0 - - - +
1020B GLY* 3.2 19.2 + - - -
1024B ASP 3.7 8.7 - - - +
1025B GLU* 1.3 83.7 - - + +
1027B GLU* 1.3 65.1 + - + +
1084C ARG* 4.8 10.3 - - - +
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Residues in contact with GLU1027 (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 VAL* 3.7 26.4 - - + +
1018B ALA 3.4 12.8 - - - +
1019B LYS* 3.9 24.4 + - + -
1020B GLY 4.6 0.4 - - - +
1025B GLU* 3.1 11.3 - - - +
1026B PRO* 1.3 86.0 - - + +
1028B THR* 1.3 66.7 + - - +
1084C ARG* 5.4 3.8 + - - -
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Residues in contact with THR1028 (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 VAL* 3.4 5.7 - - - -
1018B ALA 3.0 29.2 + - - -
1021B VAL* 3.8 17.7 - - + +
1022B VAL* 3.6 23.2 + - + +
1025B GLU* 2.7 32.6 + - - +
1027B GLU* 1.3 77.3 - - - +
1029B ARG* 1.3 75.1 + - - +
1030B VAL* 3.6 9.4 - - + +
1066B LEU* 4.8 4.0 - - + -
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Residues in contact with ARG1029 (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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1015B GLU* 3.1 27.5 + - - +
1016B GLY 3.5 10.1 - - - +
1017B VAL* 4.6 9.9 - - + +
1028B THR* 1.3 80.9 - - - +
1030B VAL* 1.3 64.6 + - - +
1066B LEU* 5.3 0.3 - - - +
1081B LEU* 3.7 35.8 + - + +
1083B THR* 3.9 21.4 - - - +
1145B GLU* 5.6 4.8 + - - -
1029C ARG* 4.7 18.8 - - - +
1145C GLU* 5.0 11.9 - - - +
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Residues in contact with VAL1030 (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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1015B GLU* 3.6 8.1 - - - +
1016B GLY 3.0 42.9 + - - +
1017B VAL 4.0 1.1 - - - +
1018B ALA* 4.0 19.3 - - + +
1021B VAL* 4.5 0.9 - - + -
1028B THR* 3.6 15.0 - - + +
1029B ARG* 1.3 79.9 - - - +
1031B ALA* 1.3 60.5 + - - +
1032B ILE* 3.9 18.8 - - + -
1066B LEU* 3.9 19.7 - - + -
1078B ILE* 3.7 26.2 - - + -
1079B MET 3.6 7.6 - - - +
1081B LEU* 3.9 8.9 - - - +
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Residues in contact with ALA1031 (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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1005B LEU* 4.3 3.1 - - + -
1013B VAL* 4.8 0.7 - - + -
1014B TYR 3.5 8.1 - - - +
1030B VAL* 1.3 75.4 - - - +
1032B ILE* 1.3 61.4 + - - +
1033B LYS 4.2 0.9 - - - -
1077B VAL 3.8 0.5 - - - +
1078B ILE* 3.5 3.8 - - - -
1079B MET* 2.9 39.8 + - + +
1080B GLU 4.4 6.5 - - - +
1081B LEU* 4.0 17.5 - - + +
1154B PHE* 3.6 35.4 - - + -
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Residues in contact with ILE1032 (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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999B ILE* 3.5 18.4 - - + -
1000B THR 3.8 11.0 - - - +
1001B MET* 3.3 36.8 - - + -
1012B MET 4.1 0.5 - - - +
1013B VAL* 3.4 3.5 - - - +
1014B TYR* 2.8 40.2 + - + +
1015B GLU 4.4 0.2 - - - -
1016B GLY* 3.9 14.4 - - - +
1030B VAL* 3.9 13.5 - - + +
1031B ALA* 1.3 77.6 - - - +
1033B LYS* 1.3 71.2 + - - +
1034B THR* 3.9 2.4 + - + +
1076B LEU* 4.0 20.9 - - + -
1077B VAL 3.5 2.7 - - - -
1078B ILE* 4.0 20.9 - - + -
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Residues in contact with LYS1033 (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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2B CCX 3.8 28.2 + - - -
1010B PHE* 4.8 3.6 - - - -
1012B MET 4.2 2.7 - - - -
1013B VAL* 4.4 9.4 - - + -
1031B ALA 5.7 0.2 - - - +
1032B ILE* 1.3 75.8 - - - +
1034B THR* 1.3 61.2 + - - +
1047B PHE* 3.8 30.7 + - + -
1050B GLU* 3.9 18.2 + - - +
1076B LEU* 3.3 6.8 - - - +
1077B VAL* 2.9 37.4 + - - +
1079B MET* 3.8 16.8 - - - -
1153B ASP 5.1 1.6 + - - -
1154B PHE* 3.6 56.7 + - + +
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Residues in contact with THR1034 (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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1001B MET* 4.8 3.1 - - + -
1010B PHE* 3.6 1.7 - - - +
1011B GLY* 3.4 21.9 + - - +
1012B MET* 2.8 34.1 + - - +
1014B TYR* 3.9 24.1 - - + -
1032B ILE* 4.1 4.3 - - + +
1033B LYS* 1.3 78.0 - - - +
1035B VAL* 1.3 68.4 + - - +
1036B ASN* 4.6 1.0 + - - -
1047B PHE* 3.9 9.2 - - - -
1074B PRO* 4.7 8.5 - - + -
1075B THR 3.3 9.6 - - - -
1076B LEU* 3.5 20.0 - - + -
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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