Contacts of the strand formed by residues 1011 - 1018 (chain D) 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 GLY1011 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007D GLN* 3.7 13.6 + - - +
1008D GLY* 2.6 40.9 + - - +
1009D SER 3.4 0.4 + - - -
1010D PHE* 1.3 82.0 - - - +
1012D MET* 1.3 55.5 + - - -
1033D LYS* 4.1 6.8 - - - +
1034D THR 3.4 13.2 - - - -
1035D VAL* 4.9 0.2 - - - -
1036D ASN* 5.6 4.3 - - - -
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Residues in contact with MET1012 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D GLU* 4.0 28.9 - - + +
1006D GLY* 3.1 26.7 - - - +
1007D GLN* 3.0 32.7 + - + +
1011D GLY* 1.3 72.1 - - - -
1013D VAL* 1.3 66.6 + - - +
1014D TYR* 3.2 40.7 - - + +
1033D LYS* 3.3 1.8 - - - -
1034D THR* 3.0 33.4 + - - +
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Residues in contact with VAL1013 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D 741 3.7 44.9 - - + +
1004D GLU* 3.7 2.3 - - - -
1005D LEU* 2.8 42.5 + - + -
1006D GLY 2.8 23.2 + - - +
1008D GLY* 4.1 10.5 - - - -
1012D MET* 1.3 72.7 - - - +
1014D TYR* 1.3 71.7 + - - +
1031D ALA* 4.2 5.6 - - + -
1032D ILE 3.3 7.0 - - - +
1033D LYS* 3.7 29.8 - - + -
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Residues in contact with TYR1014 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001D MET* 3.0 39.9 - - + -
1002D SER 5.6 0.4 - - - -
1003D ARG* 3.5 10.5 - - - +
1004D GLU* 3.8 35.5 + - + -
1005D LEU* 3.7 6.3 - - - +
1012D MET* 3.2 32.0 - - + +
1013D VAL* 1.3 76.7 - - - +
1015D GLU* 1.3 63.8 + - - +
1031D ALA* 3.2 5.4 - - - +
1032D ILE* 2.6 50.0 + - + +
1034D THR* 3.4 22.7 + - + -
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Residues in contact with GLU1015 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D 741 6.0 0.5 - - - +
1001D MET 4.0 0.5 - - - -
1002D SER* 3.0 25.9 + - - -
1003D ARG* 2.9 49.3 + - + +
1005D LEU* 3.4 23.0 - - + +
1014D TYR* 1.3 77.0 - - - +
1016D GLY* 1.3 66.0 + - - +
1029D ARG* 2.7 37.8 + - - +
1030D VAL 3.6 4.3 - - - +
1032D ILE* 4.7 0.9 - - - -
1081D LEU* 3.8 21.2 - - + +
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Residues in contact with GLY1016 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000D THR 3.2 13.2 - - - -
1001D MET* 4.4 0.7 - - - -
1002D SER* 4.1 9.4 - - - -
1015D GLU* 1.3 80.6 - - - +
1017D VAL* 1.3 67.3 + - - +
1029D ARG* 3.4 9.4 - - - +
1030D VAL* 3.0 32.3 + - - -
1032D ILE* 4.5 4.4 - - - +
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Residues in contact with VAL1017 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999D ILE* 3.7 2.8 - - - +
1000D THR* 2.9 51.6 + - + +
1002D SER* 6.2 2.2 - - - -
1016D GLY* 1.3 79.7 - - - +
1018D ALA* 1.3 64.4 + - - +
1019D LYS* 4.0 2.7 - - + +
1027D GLU* 3.5 38.8 - - + +
1028D THR 3.2 12.8 - - - +
1029D ARG* 4.8 7.6 - - + +
1030D VAL* 4.0 2.5 - - - -
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Residues in contact with ALA1018 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998D LYS 3.6 4.9 - - - -
999D ILE* 3.3 24.0 - - + -
1017D VAL* 1.3 70.6 - - - +
1019D LYS* 1.3 61.6 + - - +
1020D GLY 3.4 0.9 + - - -
1021D VAL* 3.0 34.0 - - + +
1027D GLU* 4.4 0.4 - - - -
1028D THR 2.8 26.3 + - - -
1030D VAL* 3.7 19.7 - - + -
1078D ILE* 4.4 3.8 - - + -
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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