Contacts of the helix formed by residues 699 - 713 (chain A) in PDB entry 3BDP
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 PRO 699 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A THR* 1.3 88.2 - - + +
700A ASN* 1.3 60.6 + - - +
702A ARG* 3.3 7.2 + - + +
703A ARG* 3.0 24.8 + - - +
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Residues in contact with ASN 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A THR* 3.2 7.6 + - - +
699A PRO* 1.3 80.4 - - - +
701A MET* 1.3 62.5 + - + +
703A ARG* 2.8 41.1 + - - +
704A GLN* 3.2 40.9 + - - +
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Residues in contact with MET 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ALA* 4.0 6.1 - - + +
690A PHE* 3.1 64.9 - - + -
692A VAL* 3.3 31.6 - - + -
696A GLU 3.6 8.3 - - - +
697A VAL* 4.1 3.8 - - + -
698A THR* 3.0 38.3 + - - +
700A ASN* 1.3 76.4 - - + +
702A ARG* 1.3 65.5 + - - +
704A GLN* 3.3 3.9 + - - +
705A ALA* 3.0 20.4 + - - +
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Residues in contact with ARG 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A ASP* 3.0 38.0 + - - -
682A HIS* 3.5 32.2 + - + +
683A THR* 3.5 16.9 + - - +
686A ALA* 4.2 9.6 - - - +
697A VAL* 4.3 8.9 - - + +
698A THR 3.0 11.4 + - - +
699A PRO* 3.8 9.0 - - + +
701A MET* 1.3 77.2 - - - +
703A ARG* 1.3 58.4 + - - +
705A ALA* 3.2 1.4 + - - +
706A LYS* 2.8 37.1 + - - +
910A SO4 3.0 42.7 + - - -
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Residues in contact with ARG 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A PRO 3.0 17.6 + - - +
700A ASN* 2.8 33.2 + - - +
701A MET 3.3 0.2 - - - -
702A ARG* 1.3 76.5 - - - +
704A GLN* 1.3 75.6 + - - +
706A LYS* 3.4 12.0 - - + +
707A ALA* 3.0 25.5 + - + +
724A ASN 5.1 3.2 + - - -
725A LEU* 4.0 29.1 + - - +
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Residues in contact with GLN 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A ILE* 5.4 0.2 - - - -
690A PHE* 4.2 16.0 - - + -
700A ASN* 3.2 29.9 + - - +
701A MET* 3.8 4.9 - - - +
702A ARG 3.2 0.6 - - - -
703A ARG* 1.3 97.5 - - - +
705A ALA* 1.3 59.6 + - - +
706A LYS 3.1 1.6 - - - -
707A ALA* 3.2 4.7 + - - +
708A VAL* 3.0 31.0 + - - +
725A LEU* 3.9 24.2 + - + +
727A ILE* 4.5 12.9 - - - +
735A PHE* 3.6 30.5 - - + -
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Residues in contact with ALA 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A HIS 3.3 12.8 - - - +
685A THR* 3.9 10.2 - - + +
686A ALA* 3.3 38.1 - - - +
689A ILE* 4.4 13.5 - - + -
690A PHE* 4.6 0.4 - - - -
701A MET 3.0 11.7 + - - +
702A ARG 3.8 0.7 - - - +
704A GLN* 1.3 73.9 - - - +
706A LYS* 1.3 59.8 + - - +
708A VAL* 3.3 5.0 + - - +
709A ASN* 2.9 34.1 + - - -
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Residues in contact with LYS 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A HIS* 3.6 38.6 + - + +
702A ARG* 2.8 23.4 + - - +
703A ARG* 3.4 11.0 - - + +
705A ALA* 1.3 77.4 - - - +
707A ALA* 1.3 52.7 + - - +
709A ASN* 3.1 2.8 + - - +
710A PHE* 2.7 37.5 + - + +
910A SO4 2.5 46.8 + - - +
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Residues in contact with ALA 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ARG* 3.0 11.7 + - - +
704A GLN 3.3 4.5 - - - +
706A LYS* 1.3 79.6 - - - +
708A VAL* 1.3 55.6 + - - +
710A PHE* 3.5 7.7 + - - +
711A GLY* 3.0 24.8 + - - -
721A LEU* 3.9 9.6 - - + +
724A ASN* 5.4 9.6 + - + +
725A LEU* 3.0 39.9 - - + -
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Residues in contact with VAL 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A THR* 5.2 1.1 - - + -
689A ILE* 4.6 9.4 - - + -
704A GLN 3.0 15.0 + - - +
705A ALA* 3.6 11.2 - - - +
706A LYS 3.2 0.2 - - - -
707A ALA* 1.3 76.7 - - - +
709A ASN* 1.3 52.7 + - - +
712A ILE* 2.5 42.9 + - + +
716A ILE* 4.2 10.9 - - + +
721A LEU* 4.1 17.7 - - + -
735A PHE* 4.1 30.7 - - + +
736A ILE* 5.4 1.8 - - + -
739A TYR* 3.9 35.4 - - + -
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Residues in contact with ASN 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A LEU* 4.0 23.7 - - + +
681A ILE* 3.6 10.6 + - - +
682A HIS* 2.9 33.8 - - + +
685A THR* 3.2 33.3 + - - +
705A ALA 2.9 14.8 + - - -
706A LYS 3.1 6.9 + - - +
708A VAL* 1.3 75.2 - - - +
710A PHE* 1.3 65.7 + - - +
712A ILE* 3.5 8.2 - - - +
713A VAL* 3.2 26.0 + - - +
739A TYR* 3.8 15.6 + - - -
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Residues in contact with PHE 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A HIS* 5.5 0.2 + - - -
706A LYS* 2.7 23.5 + - + +
707A ALA* 3.9 7.4 - - - +
709A ASN* 1.3 73.0 - - - +
711A GLY* 1.3 63.6 + - - +
713A VAL* 3.5 7.0 - - - +
714A TYR* 2.6 65.8 - + - -
724A ASN* 4.3 21.8 - - - -
16P 2DT 4.4 10.1 - + + -
18T A 3.7 27.1 - + - -
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Residues in contact with GLY 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A ALA 3.0 15.9 + - - -
708A VAL 3.8 0.2 - - - -
710A PHE* 1.3 83.7 - - - +
712A ILE* 1.3 69.2 + - - +
713A VAL 2.9 1.4 + - - -
714A TYR* 3.0 18.9 + - - +
716A ILE* 3.2 20.8 + - - -
717A SER 4.8 1.7 + - - -
721A LEU* 5.6 3.8 - - - -
724A ASN* 5.7 3.1 - - - -
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Residues in contact with ILE 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A LEU* 3.9 21.3 - - + -
662A LEU* 4.0 12.6 - - + -
708A VAL* 2.5 34.6 + - + +
709A ASN* 3.5 11.2 - - - +
711A GLY* 1.3 71.5 - - - +
713A VAL* 1.3 76.4 + - - +
715A GLY* 3.3 2.3 + - - -
716A ILE* 3.1 39.4 + - + +
739A TYR* 3.9 40.4 - - + +
740A PHE* 4.8 4.7 - - + -
746A VAL* 4.7 2.5 - - + -
750A MET* 4.1 19.2 - - + +
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Residues in contact with VAL 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A GLU* 4.1 28.5 - - + -
659A LEU* 4.3 15.3 - - + -
709A ASN 3.2 12.2 + - - +
710A PHE* 3.5 11.7 - - - +
711A GLY 3.1 0.2 - - - -
712A ILE* 1.3 87.6 - - - +
714A TYR* 1.3 75.9 + - + +
715A GLY* 2.6 13.0 + - - -
750A MET* 5.2 0.9 - - - +
792A MET 5.0 0.3 - - - -
793A ASN* 2.7 28.6 + - - +
796A ILE* 4.1 21.5 - - + +
797A GLN* 5.7 4.0 - - + +
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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