Contacts of the helix formed by residues 6877 - 6887 (chain A) in PDB entry 6W4H
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 ALA6877 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6870A ALA 3.2 20.6 - - - +
6876A VAL* 1.3 77.4 - - - +
6878A PRO* 1.4 65.8 - - - +
6879A GLY 3.3 2.5 - - - -
6880A THR* 3.7 18.3 - - - -
6881A ALA* 3.1 20.8 + - - +
6895A ASP* 4.2 0.4 - - - +
6901A PHE* 3.7 21.1 - - + -
6902A VAL 3.5 8.5 + - - +
6903A SER* 4.5 4.3 - - - -
6904A ASP* 5.1 2.6 + - - +
4295B VAL* 4.8 3.7 - - - +
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Residues in contact with PRO6878 (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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6839A MET* 3.8 22.9 - - - -
6841A ASN* 4.2 14.1 - - + -
6842A VAL* 3.8 21.0 - - + +
6872A SER* 4.3 2.2 - - - +
6874A LYS* 4.8 8.1 - - + -
6876A VAL* 3.4 13.9 - - + +
6877A ALA* 1.4 88.0 - - - +
6879A GLY* 1.3 61.2 - - - +
6881A ALA* 3.1 6.2 + - - +
6882A VAL* 3.1 26.4 + - - +
7102A SAM 3.5 25.4 - - - +
4295B VAL* 3.8 15.9 - - + -
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Residues in contact with GLY6879 (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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6845A TYR* 3.4 38.1 - - - -
6867A HIS* 3.9 4.3 - - - -
6878A PRO* 1.3 73.6 - - - +
6880A THR* 1.3 56.6 + - - +
6882A VAL* 3.1 4.7 + - - +
6883A LEU* 2.8 31.0 + - - +
7102A SAM 2.9 22.1 + - - -
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Residues in contact with THR6880 (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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6867A HIS* 2.9 28.4 + - - -
6870A ALA* 3.6 3.8 - - - +
6877A ALA* 3.2 14.8 + - - +
6879A GLY* 1.3 74.6 - - - +
6881A ALA* 1.3 58.8 + - - +
6883A LEU* 3.2 5.8 + - - +
6884A ARG* 2.9 28.2 + - - +
6893A LEU* 3.9 11.7 - - + -
6895A ASP* 2.7 30.2 + - - +
6903A SER* 3.5 10.5 - - - +
6904A ASP* 4.2 6.1 - - - +
6905A ALA* 3.6 20.9 - - + +
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Residues in contact with ALA6881 (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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6877A ALA 3.1 13.1 + - - +
6878A PRO 3.1 9.4 + - - +
6880A THR* 1.3 77.5 - - - +
6882A VAL* 1.3 61.2 + - - +
6884A ARG* 4.4 2.0 - - - -
6885A GLN* 3.1 6.2 + - - +
6904A ASP* 3.9 21.5 + - - +
4295B VAL* 4.0 10.8 - - + -
4297B MET* 3.6 23.9 - - - +
4322B GLY* 4.5 4.9 - - - -
4349B TYR* 2.5 29.2 + - + -
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Residues in contact with VAL6882 (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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6842A VAL* 3.7 32.1 - - + +
6845A TYR* 3.8 16.6 - - + +
6846A THR* 3.7 32.3 - - - +
6849A CYS* 4.2 4.0 - - - -
6878A PRO 3.1 14.4 + - - +
6879A GLY 3.1 6.3 + - - +
6881A ALA* 1.3 73.7 - - - +
6883A LEU* 1.3 60.6 + - - +
6885A GLN* 3.1 6.5 + - - +
6886A TRP* 2.9 26.5 + - - +
7048A PHE* 3.9 13.6 - - + -
4297B MET* 3.8 18.2 - - + -
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Residues in contact with LEU6883 (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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6845A TYR* 4.3 11.0 - - + -
6848A LEU* 6.1 1.3 - - + -
6849A CYS* 3.8 23.3 - - - -
6852A LEU* 6.1 0.4 - - + -
6865A VAL* 5.0 1.8 - - + -
6867A HIS* 3.6 45.5 - - + +
6879A GLY 2.8 15.5 + - - +
6880A THR* 3.2 6.5 + - - +
6882A VAL* 1.3 76.0 - - - +
6884A ARG* 1.3 54.7 + - - +
6886A TRP* 4.0 14.8 - - + -
6887A LEU* 2.9 47.8 + - + +
6893A LEU* 4.2 15.7 - - + -
6926A ILE* 4.2 25.6 - - + -
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Residues in contact with ARG6884 (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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6880A THR 2.9 16.3 + - - +
6881A ALA* 3.6 2.9 - - - +
6883A LEU* 1.3 76.1 - - - +
6885A GLN* 1.3 59.8 + - - +
6887A LEU* 3.7 18.8 + - - +
6888A PRO 4.6 2.8 + - - -
6889A THR* 5.9 0.8 - - - +
6890A GLY 5.4 1.5 - - - +
6891A THR* 2.8 39.3 + - - +
6893A LEU* 3.8 28.0 - - + +
6904A ASP* 3.9 23.5 + - + +
6906A ASP* 3.0 32.7 + - - -
4310B VAL 5.0 4.3 - - - +
4311B THR* 5.4 2.3 - - - +
4347B GLY* 3.9 19.7 - - - +
4349B TYR* 3.0 28.7 - - + +
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Residues in contact with GLN6885 (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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6846A THR* 5.2 1.4 + - - -
6881A ALA 3.1 7.6 + - - +
6882A VAL* 3.1 12.2 + - - +
6884A ARG* 1.3 78.6 - - - +
6886A TRP* 1.3 59.2 - - - +
6887A LEU 4.1 3.1 - - - +
7045A MET* 3.7 14.0 - - - +
7048A PHE* 3.9 21.0 - - + -
7049A PRO* 4.9 9.1 - - + +
4297B MET* 3.3 20.0 - - + +
4298B LEU 2.9 28.7 + - - +
4299B CYS* 4.6 2.6 - - - +
4311B THR* 4.5 13.7 - - - +
4312B PRO* 3.7 31.1 - - + +
4349B TYR* 2.9 19.8 + - + +
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Residues in contact with TRP6886 (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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6849A CYS* 3.5 38.2 + - + -
6852A LEU* 3.7 37.5 - - + -
6853A ASN* 2.8 20.5 + - - -
6857A LEU* 3.8 15.9 - - + -
6882A VAL 2.9 15.5 + - - +
6883A LEU* 3.7 11.4 - - + +
6885A GLN* 1.3 77.8 - - - +
6887A LEU* 1.3 91.5 + - + +
6888A PRO* 3.8 0.3 - - - +
6924A LEU* 3.7 15.7 - - + -
7048A PHE* 3.3 38.6 - + + -
7049A PRO* 3.7 3.7 - - - +
7050A LEU* 2.9 57.7 + - + +
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Residues in contact with LEU6887 (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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6863A MET* 4.2 10.1 - - + -
6865A VAL* 3.7 43.1 - - + -
6883A LEU* 2.9 33.2 + - + +
6884A ARG* 3.7 18.5 + - - +
6885A GLN 3.6 2.6 - - - +
6886A TRP* 1.3 103.1 - - + +
6888A PRO* 1.3 72.4 - - + +
6889A THR* 3.6 1.6 + - - -
6891A THR* 3.8 17.7 - - + +
6893A LEU* 4.2 13.0 - - + -
6924A LEU* 4.5 0.7 - - + -
7050A LEU* 4.0 13.7 - - + -
4311B THR* 5.9 1.9 - - - +
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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