Contacts of the strand formed by residues 1029 - 1035 (chain J) in PDB entry 3F5P
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 ARG1029 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003J ARG* 5.6 2.2 - - - +
1015J GLU* 2.5 30.8 + - + -
1016J GLY 3.5 7.6 - - - +
1017J VAL* 4.8 9.9 - - + +
1028J THR* 1.3 81.0 - - - +
1030J VAL* 1.3 63.0 + - - +
1080J GLU* 4.8 0.3 - - - -
1081J LEU* 3.1 37.4 + - + +
1083J THR* 3.6 21.6 - - - +
1145J GLU* 4.3 13.3 + - - +
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Residues in contact with VAL1030 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015J GLU* 3.7 1.4 - - - +
1016J GLY 2.8 44.8 + - - +
1018J ALA* 3.8 21.3 - - + +
1028J THR* 3.6 11.2 - - + +
1029J ARG* 1.3 79.0 - - - +
1031J ALA* 1.3 59.3 + - - +
1032J ILE* 3.6 25.6 - - + -
1066J LEU* 3.5 32.5 - - + -
1078J ILE* 3.5 13.0 - - + -
1079J MET 3.3 8.5 - - - +
1081J LEU* 3.6 14.9 - - - +
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Residues in contact with ALA1031 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J 741 3.4 56.8 - - + +
1005J LEU* 4.8 0.9 - - + -
1013J VAL* 4.2 3.6 - - + -
1014J TYR 3.4 8.7 - - - +
1030J VAL* 1.3 74.5 - - - +
1032J ILE* 1.3 60.2 + - - +
1078J ILE* 3.5 3.1 - - - -
1079J MET 2.7 37.9 + - - +
1081J LEU* 4.1 5.1 - - + +
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Residues in contact with ILE1032 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J 741 3.9 1.6 - - - -
999J ILE* 3.4 26.5 - - + -
1000J THR 4.1 1.6 - - - +
1001J MET* 3.6 37.0 - - + -
1012J MET 3.8 0.9 - - - +
1013J VAL* 3.4 1.5 - - - +
1014J TYR* 2.6 41.5 + - - +
1016J GLY* 3.9 14.4 - - - -
1017J VAL 4.7 0.4 - - - +
1030J VAL* 3.6 23.6 - - + -
1031J ALA* 1.3 80.8 - - - +
1033J LYS* 1.3 62.2 + - - +
1034J THR 4.0 0.2 + - - -
1076J LEU* 4.1 27.1 - - + -
1077J VAL 3.3 7.2 - - - +
1078J ILE* 4.2 7.9 - - + -
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Residues in contact with LYS1033 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J 741 3.1 52.8 + - + +
1008J GLY* 3.5 1.8 - - - -
1009J SER* 2.6 44.3 + - - +
1010J PHE* 3.0 26.0 - - - +
1011J GLY 3.4 12.1 - - - +
1012J MET 3.3 9.4 - - - +
1013J VAL* 4.1 12.3 - - + +
1032J ILE* 1.3 73.4 - - - +
1034J THR* 1.3 69.0 + - - +
1035J VAL* 4.8 1.6 - - + +
1047J PHE* 4.2 8.3 - - + -
1075J THR 3.4 5.9 - - - +
1076J LEU* 3.5 2.4 - - - -
1077J VAL* 3.0 30.7 + - + +
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Residues in contact with THR1034 (chain J).
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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1106B PRO 5.5 0.5 + - - -
1108B SER* 4.4 17.8 - - - -
1001J MET* 4.0 26.2 - - + -
1011J GLY* 3.2 26.0 - - - -
1012J MET* 2.9 23.1 + - - +
1014J TYR* 4.2 10.5 - - + -
1032J ILE 4.8 0.4 - - - +
1033J LYS* 1.3 74.1 - - - +
1035J VAL* 1.3 61.1 + - - +
1036J ASN* 4.0 6.3 + - - +
1074J PRO* 4.5 12.3 - - + -
1075J THR 3.6 3.6 - - - -
1076J LEU* 3.6 23.6 - - + -
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Residues in contact with VAL1035 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010J PHE* 4.3 26.0 - - + +
1011J GLY* 5.0 0.2 - - - -
1033J LYS* 4.8 2.7 - - + +
1034J THR* 1.3 76.7 - - - +
1036J ASN* 1.3 64.4 + - - +
1039J ALA* 3.6 27.6 - - + -
1043J GLU 6.0 0.4 - - - -
1044J ARG* 3.3 27.7 + - + +
1047J PHE* 3.3 40.2 - - + -
1074J PRO* 3.5 1.5 - - - +
1075J THR* 3.2 36.3 + - - +
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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