Contacts of the helix formed by residues 717 - 722 (chain M) in PDB entry 2W4G
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 TYR 717 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C LYS* 1.4 57.7 - - + +
97C GLU 2.6 0.4 - - - -
98C GLY* 3.1 15.3 - - - +
715M VAL 3.5 0.8 + - - -
716M LEU* 1.3 70.0 - - - +
718M ALA 1.3 47.0 - - - +
720M PHE* 3.8 0.2 - - - -
740M SER 3.1 15.7 - - - +
741M LYS* 3.9 38.4 - - + +
744M SER* 2.9 31.2 - - - -
760M PHE* 3.1 36.9 - + - +
761M GLY 3.3 24.7 + - - -
762M HIS 4.8 1.3 - - - -
763M THR* 3.6 20.0 - - - +
764M LYS* 3.6 6.3 - - - -
765M VAL* 3.4 25.7 - - + +
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Residues in contact with ALA 718 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ASP* 2.2 6.9 - - - -
96C LYS* 0.8 174.9 + - - +
97C GLU* 0.9 153.5 - - + +
98C GLY 2.9 0.4 - - - +
716M LEU* 3.5 0.8 - - + +
717M TYR* 1.3 63.2 - - - +
719M ASP* 1.4 51.0 - - - +
720M PHE 2.9 1.2 + - - -
721M LYS 2.8 0.9 + - - -
722M GLN* 3.0 5.2 + - - +
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Residues in contact with ASP 719 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LYS 1.4 39.0 + - - -
97C GLU* 3.9 15.6 - - - +
715M VAL* 4.1 7.0 - - + +
716M LEU* 3.2 36.9 - - + +
718M ALA* 1.4 41.9 - - - +
720M PHE* 1.4 56.5 + - - -
722M GLN* 4.8 2.9 - - - +
723M ARG* 3.7 21.5 + - - +
724M TYR* 4.9 1.6 - - - -
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Residues in contact with PHE 720 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLU 3.7 2.9 - - - -
92C ARG* 1.9 31.1 - - + +
93C VAL* 2.0 72.5 - - + +
96C LYS* 0.5 333.9 + - + +
715M VAL* 3.3 31.4 - - + -
716M LEU 2.8 3.6 + - - +
717M TYR* 3.0 1.1 - - + +
719M ASP* 1.4 68.4 - - - +
721M LYS* 1.3 48.5 - - - -
724M TYR* 3.5 12.1 - + - -
744M SER* 3.3 0.2 - - - -
748M LEU* 3.6 30.5 - - + -
765M VAL* 5.5 0.7 - - + -
767M PHE* 3.6 26.2 - + - -
772M LEU* 5.2 0.7 - - + -
775M LEU* 4.1 8.7 - - + -
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Residues in contact with LYS 721 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ARG* 1.8 21.3 - - + +
93C VAL 2.9 1.3 - - - -
94C PHE* 1.4 49.1 + - - -
95C ASP 1.3 89.1 - - - +
96C LYS* 1.6 32.8 - - - +
99C ASN 3.2 7.6 - - - +
100C GLY* 1.3 46.9 + - - -
101C THR* 0.5 187.0 - - - +
139C TYR* 2.3 37.7 - - + -
720M PHE 1.3 57.0 - - - -
722M GLN 1.3 19.3 - - - -
725M ARG 2.7 0.2 + - - -
738M MET 4.5 0.2 - - - -
739M ASP 4.5 0.2 - - - +
740M SER 4.5 0.2 - - - +
743M ALA* 3.9 0.7 - - + -
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Residues in contact with GLN 722 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 0.7 142.3 + - - +
95C ASP* 1.2 105.9 + - + +
96C LYS 2.3 1.6 - - - +
97C GLU* 4.3 15.7 + - - +
103C MET* 5.9 1.6 - - - +
106C GLU* 2.3 34.5 + - - +
718M ALA 3.8 5.2 - - - +
719M ASP* 5.2 3.1 - - - +
721M LYS 1.3 20.4 - - - +
723M ARG* 1.3 56.8 + - + +
779M ARG* 4.9 2.6 + - - +
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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