Contacts of the strand formed by residues 938 - 948 (chain B) in PDB entry 5JPM
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 ALA 938 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844B ARG* 4.8 7.9 - - - +
937B GLY* 1.3 74.4 - - - -
939B ILE* 1.3 70.1 + - - +
940B HIS* 3.4 6.2 + - - +
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Residues in contact with ILE 939 (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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934B GLU* 5.2 9.2 - - - +
937B GLY 5.7 2.0 - - - +
938B ALA* 1.3 78.1 - - - +
940B HIS* 1.3 69.8 + - - +
941B ARG* 4.4 15.9 - - + -
974B PHE* 6.4 2.0 - - + -
1005B ARG* 6.3 0.7 - - - +
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Residues in contact with HIS 940 (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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938B ALA 3.4 5.4 + - - +
939B ILE* 1.3 78.5 - - - +
941B ARG* 1.3 78.6 + - - +
942B GLU* 4.2 11.1 + - + +
965B ASP* 5.1 13.6 + - - -
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Residues in contact with ARG 941 (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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939B ILE* 4.4 16.2 - - + -
940B HIS* 1.3 91.0 + - - +
942B GLU* 1.3 60.6 + - - +
943B GLU* 2.8 39.4 + - - +
1005B ARG* 3.3 38.4 - - - +
1295B PHE* 5.0 6.0 - - - +
1296B GLN* 3.0 32.9 + - - +
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Residues in contact with GLU 942 (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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940B HIS* 4.2 13.0 + - + +
941B ARG* 1.3 74.3 - - - +
943B GLU* 1.3 65.2 + - - +
944B LEU* 4.1 30.4 + - + +
962B GLY 5.6 0.5 - - - +
963B ASN* 3.0 31.3 + - - +
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Residues in contact with GLU 943 (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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941B ARG* 2.8 43.7 + - - +
942B GLU* 1.3 78.1 - - - +
944B LEU* 1.3 69.8 + - - +
945B VAL* 5.4 2.5 - - + -
1005B ARG* 4.8 2.4 + - - -
1256B GLN* 3.8 26.3 - - + +
1294B SER* 3.5 13.9 - - - -
1295B PHE* 3.0 42.4 + - + +
1296B GLN* 5.7 0.2 - - - +
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Residues in contact with LEU 944 (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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942B GLU* 4.1 29.9 + - + +
943B GLU* 1.3 82.0 - - - +
945B VAL* 1.3 65.6 + - - +
946B TYR* 4.2 32.3 + - + +
960B ILE* 6.2 1.8 - - + -
961B PRO* 6.4 0.4 - - + -
1253B PRO* 4.3 20.2 - - + -
1254B MET 5.3 4.5 - - - +
1255B PRO* 6.3 1.6 - - + -
1256B GLN* 5.5 3.4 - - + +
1295B PHE* 5.7 4.3 - - - -
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Residues in contact with VAL 945 (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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943B GLU* 5.4 2.5 - - + -
944B LEU* 1.3 79.4 - - - +
946B TYR* 1.3 60.7 + - - +
1253B PRO* 3.5 3.3 - - - +
1254B MET* 2.8 43.4 + - + +
1256B GLN* 3.3 23.6 - - - +
1291B ARG* 3.2 30.1 - - + +
1293B GLY 3.8 21.3 - - - +
1294B SER* 5.3 4.7 - - - +
1295B PHE* 5.6 4.5 - - + +
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Residues in contact with TYR 946 (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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944B LEU* 4.2 23.3 - - + +
945B VAL* 1.3 80.8 - - - +
947B GLU* 1.3 62.5 + - - +
948B LEU* 3.6 12.9 + - + +
958B LEU* 3.9 24.7 - - + -
959B GLU 4.8 3.1 - - - -
960B ILE* 4.1 37.2 - - + +
961B PRO* 3.9 21.5 - - - +
1250B PRO 4.7 0.9 - - - -
1251B SER 3.4 25.8 - - - -
1252B ASP 3.9 3.1 - - - -
1253B PRO* 3.4 43.2 - - + +
1254B MET* 4.8 1.3 - - - +
1291B ARG* 5.6 3.0 - - - +
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Residues in contact with GLU 947 (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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945B VAL 4.3 0.6 + - - -
946B TYR* 1.3 72.1 - - - +
948B LEU* 1.3 72.9 + - - +
949B ASN* 3.4 29.6 + - + +
955B GLY* 5.5 3.1 - - - +
958B LEU* 4.5 6.9 - - - +
1226B ASP* 3.7 12.9 - - - +
1227B ASN* 4.6 3.8 + - - -
1250B PRO* 4.1 37.7 + - + +
1252B ASP 5.4 2.0 + - - -
1254B MET* 4.9 10.8 - - + +
1291B ARG* 2.7 52.2 + - - +
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Residues in contact with LEU 948 (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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946B TYR* 3.6 11.8 + - + +
947B GLU* 1.3 80.7 - - - +
949B ASN* 1.3 60.8 + - - +
950B PRO* 3.9 7.5 - - + +
955B GLY 5.4 2.0 - - - +
958B LEU* 4.4 24.5 - - + -
980B VAL* 3.6 31.2 - - + -
981B THR 4.7 11.4 - - - +
1327B LEU* 4.6 28.6 - - + +
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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