Contacts of the strand formed by residues 1023 - 1032 (chain B) in PDB entry 5JP2
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 VAL1023 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018B GLN 4.2 0.2 - - - +
1019B ARG* 3.5 4.6 - - - +
1020B SER* 3.0 39.6 + - - +
1021B GLY 3.3 0.2 - - - -
1022B THR* 1.3 84.2 - - - +
1024B THR* 1.3 69.4 + - - +
1025B ARG* 4.2 2.1 + - + +
1095B SER* 4.5 12.6 - - - +
1096B TRP 3.3 10.5 - - - +
1097B GLN* 3.9 25.4 - - + +
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Residues in contact with THR1024 (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 CYS* 4.5 9.9 - - - -
1018B GLN 3.6 9.6 - - - +
1019B ARG* 3.5 35.9 + - + +
1022B THR 4.4 4.5 + - - -
1023B VAL* 1.3 74.2 - - - +
1025B ARG* 1.3 66.9 + - - +
1095B SER* 3.1 6.5 - - - -
1096B TRP* 2.8 71.3 + - + +
1098B CYS* 5.2 5.7 - - - +
1107B PRO* 5.2 1.6 - - + -
1152B LEU* 5.1 0.2 - - + -
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Residues in contact with ARG1025 (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 CYS* 3.4 8.3 - - - -
1018B GLN* 2.9 68.0 + - + +
1023B VAL* 4.2 2.9 - - + -
1024B THR* 1.3 75.8 - - - +
1026B VAL* 1.3 65.4 + - - +
1027B SER* 4.1 13.5 - - - -
1093B CYS* 3.9 32.1 - - - +
1094B ALA 3.5 10.8 - - - +
1095B SER* 4.2 9.6 - - - -
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Residues in contact with VAL1026 (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 ALA* 5.1 0.2 - - + -
1016B GLU 3.5 10.1 - - - +
1017B CYS* 4.2 6.1 - - - -
1025B ARG* 1.3 78.2 - - - +
1027B SER* 1.3 66.1 + - - +
1049B LEU* 4.0 17.0 - - + -
1075B TRP* 6.0 0.4 - - + -
1093B CYS* 3.1 6.1 - - - +
1094B ALA* 2.9 45.2 + - + +
1096B TRP* 3.6 24.2 - - + -
1107B PRO* 4.4 7.0 - - + +
1109B LEU* 4.0 26.9 - - + -
1150B CYS* 4.4 16.6 - - - -
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Residues in contact with SER1027 (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 SER 3.9 0.5 + - - +
1015B ALA* 3.2 6.6 - - - +
1016B GLU* 2.9 48.4 + - - +
1018B GLN* 5.3 4.2 + - - -
1025B ARG* 4.1 17.0 - - - -
1026B VAL* 1.3 80.0 - - - +
1028B LEU* 1.3 60.8 + - - +
1029B ASP* 5.0 5.9 + - - -
1091B THR* 5.3 4.5 - - - -
1092B LEU 3.4 6.3 - - - -
1093B CYS* 3.9 12.3 - - - -
1109B LEU* 5.2 0.4 - - - -
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Residues in contact with LEU1028 (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* 4.2 16.8 - - + -
1014B SER 3.5 18.2 - - - +
1015B ALA* 4.1 4.9 - - + -
1027B SER* 1.3 74.0 - - - +
1029B ASP* 1.3 72.3 + - - +
1030B TYR* 4.1 10.2 + - + -
1047B VAL* 4.2 28.5 - - + -
1091B THR* 3.2 4.0 - - - -
1092B LEU* 2.7 55.4 + - + +
1109B LEU* 4.2 17.7 - - + -
1111B VAL* 4.7 3.4 - - + -
1148B ALA* 3.8 28.5 - - + -
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Residues in contact with ASP1029 (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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1085A HIS* 4.4 16.7 - - + +
1012B LEU 3.6 0.5 - - - +
1013B LEU* 3.5 4.0 - - - -
1014B SER* 2.9 49.0 + - - +
1016B GLU* 5.5 5.4 - - - +
1027B SER* 5.0 6.1 + - - -
1028B LEU* 1.3 76.7 + - - +
1030B TYR* 1.3 60.2 + - - +
1090B GLY 3.6 6.3 - - - +
1091B THR* 3.0 26.4 + - - -
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Residues in contact with TYR1030 (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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1085A HIS* 4.1 3.3 + - - -
1011B LEU* 4.2 8.1 - - + -
1012B LEU 3.2 8.1 - - - +
1013B LEU* 4.0 15.7 - - + -
1028B LEU* 4.3 12.3 - - + -
1029B ASP* 1.3 76.3 - - - +
1031B HIS* 1.3 61.7 + - - +
1047B VAL* 5.8 1.1 - - + -
1077B LEU* 3.6 36.1 - - + +
1080B LEU* 4.1 29.2 - - + +
1088B GLY 4.4 5.4 - - - -
1089B SER* 3.4 10.3 + - - -
1090B GLY* 3.1 62.8 + - - +
1091B THR* 3.7 6.1 + - - -
1092B LEU* 3.9 18.6 - - + -
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Residues in contact with HIS1031 (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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1031A HIS* 2.8 20.9 + + - -
1033A CYS* 2.9 11.6 - - - -
1034A PRO* 4.0 14.1 - - + -
1085A HIS* 4.1 15.9 - + + -
1201A ZN 1.9 37.7 - - - -
1010B PRO 4.1 0.7 - - - +
1011B LEU* 3.5 5.4 - - - +
1012B LEU* 2.9 50.5 + - + +
1030B TYR* 1.3 77.9 - - - +
1032B CYS* 1.3 65.1 + - - +
1033B CYS* 3.1 15.9 + - + +
1034B PRO* 5.7 0.4 - - + -
1036B THR* 4.9 0.3 + - - -
1088B GLY 4.0 0.2 - - - -
1089B SER* 3.1 18.9 + - - -
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Residues in contact with CYS1032 (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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1010B PRO 4.0 4.9 - - - -
1011B LEU* 4.2 11.0 - - + -
1031B HIS* 1.3 79.3 + - - +
1033B CYS* 1.3 61.5 + - - +
1034B PRO* 4.5 0.3 - - - +
1037B ALA* 4.1 10.3 - - - -
1042B LEU* 4.0 23.1 - - - -
1080B LEU* 4.3 9.9 - - + -
1081B SER 3.9 4.3 - - - -
1082B PRO* 3.7 39.1 - - - +
1084B ASN 5.4 0.3 - - - +
1088B GLY* 3.0 31.0 + - - +
1089B SER* 4.9 0.2 + - - -
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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