Contacts of the strand formed by residues 1001 - 1010 (chain B) in PDB entry 4CEJ
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 ALA1001 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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955B LEU* 3.3 24.5 - - + +
957B LEU* 3.7 30.3 - - + -
990B ILE* 3.9 17.4 - - + +
993B SER* 3.1 19.6 + - - -
1000B ARG* 1.3 87.6 + - - +
1002B THR* 1.3 67.8 + - - +
1003B PRO* 4.3 0.3 - - - +
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Residues in contact with THR1002 (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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953B LYS* 4.7 15.5 + - + +
954B GLY* 5.5 0.5 - - - -
955B LEU 2.9 6.3 + - - -
956B LEU* 3.4 23.4 - - + +
957B LEU 3.3 14.0 + - - -
990B ILE* 3.7 3.8 - - - -
1001B ALA* 1.3 79.4 + - - +
1003B PRO* 1.3 81.7 - - + +
1004B ALA 3.0 4.0 + - - -
1042B LEU* 4.2 7.2 - - + -
1082B GLU* 3.2 35.0 + - + +
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Residues in contact with PRO1003 (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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957B LEU 3.8 4.7 - - - +
986B LEU* 3.9 17.9 - - + -
990B ILE* 3.5 32.7 - - + -
1001B ALA 4.3 0.2 - - - +
1002B THR* 1.3 86.3 - - + -
1004B ALA* 1.3 61.4 + - - +
1005B GLY 3.6 0.7 - - - -
1042B LEU* 3.4 28.1 - - - +
1082B GLU* 5.3 5.8 - - + -
1085B PHE* 3.6 29.2 - - + -
1086B ASP* 5.1 9.0 - - - +
1089B THR* 6.0 1.3 - - - +
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Residues in contact with ALA1004 (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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909B PHE* 3.5 32.8 - - + -
956B LEU* 4.1 11.0 - - + -
957B LEU 2.7 28.1 + - - +
958B ARG* 3.9 2.2 - - + -
1002B THR 3.0 1.6 + - - -
1003B PRO* 1.3 73.3 - - - +
1005B GLY* 1.3 57.1 + - - +
1041B LEU* 3.8 0.9 - - - -
1042B LEU* 3.2 25.2 + - - +
1047B VAL* 3.8 9.1 - - + +
1051B MET* 3.7 13.6 - - + +
1085B PHE* 4.1 1.1 - - - -
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Residues in contact with GLY1005 (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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957B LEU 3.8 1.0 + - - -
958B ARG* 3.2 9.0 - - - +
959B ILE 3.0 23.2 + - - -
986B LEU* 4.4 3.6 - - - +
1003B PRO* 3.6 1.6 - - - +
1004B ALA* 1.3 81.2 - - - +
1006B VAL* 1.3 66.1 + - - +
1007B LEU* 4.2 2.9 - - - -
1040B LEU 3.2 13.9 - - - -
1041B LEU* 4.2 0.4 - - - -
1051B MET* 4.5 4.7 - - - -
1085B PHE* 3.6 12.1 - - - -
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Residues in contact with VAL1006 (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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959B ILE* 3.4 11.2 - - + -
969B LEU* 4.0 19.1 - - + -
982B MET* 3.6 41.0 - - + +
983B LEU* 4.3 10.5 - - + -
986B LEU* 4.0 21.8 - - + -
1005B GLY* 1.3 76.8 - - - +
1007B LEU* 1.3 62.7 + - - +
1008B TYR* 4.9 0.6 - - + -
1039B GLY* 3.2 4.9 - - - -
1040B LEU* 2.8 55.0 + - + +
1085B PHE* 4.4 3.8 - - + -
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Residues in contact with LEU1007 (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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958B ARG* 3.4 41.7 - - - +
959B ILE 2.7 14.1 + - - +
960B VAL* 3.2 7.5 - - + +
961B ALA 2.8 31.2 + - - -
982B MET* 3.3 7.4 - - - +
1005B GLY 4.9 1.1 - - - -
1006B VAL* 1.3 81.7 - - - +
1008B TYR* 1.3 54.6 + - - +
1037B MET* 4.1 24.2 - - + +
1038B LYS 3.6 11.4 - - - +
1039B GLY* 4.7 0.2 - - - -
1041B LEU* 3.7 28.5 - - + -
1051B MET* 3.8 9.4 - - + -
1063B ILE* 3.6 23.6 - - + -
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Residues in contact with TYR1008 (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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961B ALA* 3.4 10.1 - - + +
963B LYS* 3.5 45.9 + - + -
965B SER 5.7 1.8 - - - +
967B LYS 4.6 10.5 - - - +
968B GLY* 3.4 39.7 + - - -
969B LEU* 3.4 30.7 - - + +
979B ALA* 5.4 2.4 - - - +
982B MET* 3.1 37.6 - - + +
1006B VAL 5.0 0.7 - - - -
1007B LEU* 1.3 75.2 - - - +
1009B PHE* 1.3 61.6 + - - +
1010B HIS 4.1 1.5 + - - +
1037B MET* 3.3 28.3 - - - +
1038B LYS* 2.8 22.7 + - + +
1039B GLY* 4.2 3.6 - - - -
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Residues in contact with PHE1009 (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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896B VAL* 3.9 23.6 - - + -
899B ILE* 3.5 24.5 - - + -
900B LEU* 3.9 20.4 - - + -
903B HIS* 3.7 28.0 - + - -
945B ARG* 5.4 0.2 - - - -
960B VAL* 4.3 8.5 - - + -
961B ALA 2.8 10.4 + - - +
962B TYR* 3.5 27.5 - + + -
963B LYS* 2.8 27.7 + - - +
1008B TYR* 1.3 74.2 - - - +
1010B HIS* 1.3 73.9 + - - +
1011B ILE* 3.3 13.2 + - + -
1035B PHE* 3.9 13.7 - + - -
1037B MET* 3.7 24.5 - - + +
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Residues in contact with HIS1010 (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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172A ARG* 5.0 1.2 + - - -
963B LYS 3.2 4.7 - - - -
964B SER 3.6 32.2 + - - -
965B SER* 3.8 13.2 + - - +
966B ASP* 3.9 28.5 - - + +
1008B TYR 4.1 2.6 + - - -
1009B PHE* 1.3 72.8 - - - +
1011B ILE* 1.3 65.4 + - - +
1012B HIS* 3.0 58.9 + + + +
1034B LYS 5.1 4.5 + - - +
1035B PHE* 3.5 21.9 + - + +
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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