Contacts of the helix formed by residues 707 - 714 (chain A) in PDB entry 3W5D
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 ASP 707 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A LYS* 3.3 35.8 + - + +
701A THR 5.2 0.2 - - - +
702A GLY* 3.5 16.6 - - - -
703A ASP* 2.9 27.3 + - - +
704A GLY* 2.8 15.0 + - - +
706A ASN* 1.3 85.4 + - - +
708A ALA* 1.3 68.7 + - - +
709A PRO* 3.2 3.6 - - - -
710A ALA* 2.9 20.8 + - + +
711A LEU* 3.0 15.1 + - + -
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Residues in contact with ALA 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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235A ILE* 4.6 0.4 - - + -
239A MET* 3.6 29.8 - - + +
704A GLY 3.2 6.9 + - - +
705A VAL* 3.2 20.6 - - - +
707A ASP* 1.3 75.5 - - - +
709A PRO* 1.3 65.8 - - + +
711A LEU* 3.3 13.9 + - + +
712A LYS* 2.9 25.6 + - - +
726A VAL* 4.4 9.9 - - + +
727A ALA* 5.2 0.4 - - - -
730A ALA* 4.1 8.8 - - + +
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Residues in contact with PRO 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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235A ILE* 4.2 26.2 - - + +
238A GLN* 4.2 32.1 - - + +
239A MET* 4.1 10.8 - - + +
242A THR* 4.8 4.3 + - - +
685A SER* 4.1 13.9 - - - +
705A VAL 3.6 9.2 - - - +
706A ASN* 3.7 9.9 - - - +
707A ASP 3.3 4.9 - - - -
708A ALA* 1.3 92.6 - - + +
710A ALA* 1.3 55.1 + - - +
712A LYS* 3.2 5.0 + - + +
713A LYS* 2.9 28.1 + - - +
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Residues in contact with ALA 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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684A LYS* 3.8 33.0 - - + +
685A SER* 3.9 18.5 + - - +
688A VAL* 4.7 3.0 - - + +
700A MET* 4.2 15.3 - - + -
707A ASP* 2.9 12.0 + - + +
709A PRO* 1.3 72.2 - - - +
711A LEU* 1.3 68.2 + - + +
713A LYS* 3.0 4.3 + - - +
714A ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 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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700A MET* 3.6 10.5 - - + +
701A THR 4.1 1.3 - - - -
702A GLY* 3.7 11.4 - - - +
707A ASP* 3.0 18.4 + - + +
708A ALA* 3.5 18.4 - - - +
710A ALA* 1.3 75.9 - - - +
712A LYS* 1.3 51.6 + - - +
714A ALA* 3.6 1.8 - - - +
717A GLY* 3.5 14.8 - - - -
718A ILE 3.3 42.2 - - - +
719A ALA* 4.8 0.7 - - + -
727A ALA* 3.3 46.9 - - + +
730A ALA* 3.6 14.1 - - + +
731A SER* 4.6 1.1 - - - -
1001A NA 2.6 27.5 - - - -
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Residues in contact with LYS 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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115A ALA* 5.7 3.4 - - + -
116A ILE* 4.7 11.9 - - - -
239A MET* 3.1 43.2 + - + +
240A ALA 5.2 0.2 + - - -
242A THR* 2.7 38.5 + - + +
244A GLN* 3.2 45.2 - - - +
708A ALA 2.9 17.4 + - - +
709A PRO* 3.6 5.8 - - + +
711A LEU* 1.3 75.9 - - - +
713A LYS* 1.3 65.7 + - - +
714A ALA 3.4 0.2 - - - +
730A ALA* 3.9 13.2 + - + +
1001A NA 3.1 12.4 - - - -
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Residues in contact with LYS 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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242A THR* 3.9 26.8 - - + +
244A GLN* 5.8 0.9 - - - +
685A SER* 3.9 19.9 + - - +
688A VAL* 3.4 23.1 - - + -
689A GLU* 3.3 42.7 + - + +
692A GLN* 3.3 24.0 + - - +
709A PRO 2.9 14.8 + - - +
710A ALA* 3.0 7.0 + - - +
712A LYS* 1.3 74.7 - - - +
714A ALA* 1.3 68.6 + - - +
715A GLU* 3.5 1.0 + - - +
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Residues in contact with ALA 714 (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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688A VAL* 3.7 18.2 - - + +
698A THR* 3.4 17.3 - - - +
700A MET* 3.8 24.2 - - + -
710A ALA 2.9 18.5 + - - +
711A LEU 4.4 1.8 - - - +
712A LYS 3.4 0.3 - - - +
713A LYS* 1.3 76.6 - - - +
715A GLU* 1.3 61.5 + - - +
716A ILE 3.3 8.1 - - - +
1001A NA 2.5 30.5 - - - -
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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