Contacts of the strand formed by residues 78 - 82 (chain P) in PDB entry 3C5W
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 VAL 78 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P PRO* 1.3 70.9 - - - +
79P LEU* 1.3 72.4 + - - +
80P LEU* 3.7 4.2 + - + +
106P ARG* 3.3 38.3 - - + +
108P VAL* 3.8 28.9 - - + +
143P TYR* 4.0 13.0 - - + +
148P PRO* 4.0 16.8 - - + -
149P PRO 2.7 14.5 + - - +
150P ILE* 3.1 20.0 - - + -
151P MET 2.8 25.3 + - - -
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Residues in contact with LEU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P PRO* 3.9 14.4 - - + +
78P VAL* 1.3 78.5 - - - +
80P LEU* 1.3 62.7 + - - +
81P LEU* 3.6 15.0 + - + +
95P PHE* 4.6 2.2 - - + -
99P ILE* 3.7 29.4 - - + -
105P CYS* 4.0 8.5 - - + -
106P ARG 2.7 12.5 + - - +
107P ILE* 3.7 24.7 - - + -
108P VAL 3.0 22.9 + - - +
151P MET* 3.5 18.6 - - + +
153P ILE* 4.2 18.8 - - + -
363P VAL* 4.6 2.5 - - + -
367P LEU* 4.2 24.2 - - + -
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Residues in contact with LEU 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P VAL* 3.7 7.6 + - + -
79P LEU* 1.3 70.3 - - - +
81P LEU* 1.3 60.3 - - - +
82P LEU* 4.4 6.7 - - + -
108P VAL* 3.4 33.2 - - + +
110P LEU* 4.4 17.9 - - + -
135P VAL* 3.8 22.7 - - + +
138P VAL* 5.8 3.6 - - + -
139P VAL* 3.8 24.9 - - + -
150P ILE* 4.0 16.8 - - + -
151P MET 2.8 13.4 + - - +
152P LEU* 3.6 20.8 - - + +
153P ILE 2.9 26.7 + - - +
171P VAL* 4.9 2.7 - - + -
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Residues in contact with LEU 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P LEU* 3.6 18.6 - - + +
80P LEU* 1.3 76.1 - - - +
82P LEU* 1.3 66.8 + - - +
92P TRP* 3.5 51.3 + - + -
95P PHE* 4.1 13.0 - - + -
96P THR* 4.2 0.4 - - - +
107P ILE* 3.8 29.8 - - + -
108P VAL 2.9 13.1 + - - +
109P ALA* 3.9 4.7 - - + -
110P LEU 3.1 24.6 + - - +
153P ILE* 3.4 38.1 - - + -
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Residues in contact with LEU 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P LEU* 4.4 9.0 - - + -
81P LEU* 1.3 82.4 - - - +
83P HIS* 1.3 60.0 + - - +
92P TRP* 3.4 4.6 - - - -
110P LEU* 4.0 28.3 - - + -
112P LEU* 4.2 10.5 - - + -
135P VAL* 4.1 18.8 - - + -
152P LEU* 4.2 11.7 - - + -
153P ILE 2.8 14.1 + - - +
154P GLY* 3.4 0.2 - - - -
155P HIS 2.8 31.9 + - - -
158P GLY* 3.5 27.3 - - - +
161P ILE* 4.2 13.9 - - + -
162P ALA* 3.5 26.2 - - + +
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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
------------------------------------------------------------
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