Contacts of the strand formed by residues 75 - 79 (chain B) in PDB entry 3GUC
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 ALA 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B PHE* 1.3 75.2 - - - +
76B VAL* 1.3 63.7 + - - +
99B LYS* 3.2 23.6 - - + -
101B LEU* 4.4 6.3 - - + -
168B GLY* 4.0 11.0 - - - -
169B LEU 3.7 25.3 - - - +
175B VAL* 3.8 4.3 - - - +
176B ASP* 2.8 39.3 + - - +
177B LEU 3.7 0.9 + - - -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA* 1.3 77.6 - - - +
77B ALA* 1.3 74.6 + - - +
78B ILE* 4.0 5.8 - - + -
92B LEU* 4.6 2.7 - - + -
97B ILE* 4.0 22.9 - - + -
99B LYS 2.9 6.7 + - - -
100B LEU* 3.3 19.3 - - + +
101B LEU* 2.9 25.3 + - - +
177B LEU* 3.4 17.3 - - + +
179B LEU* 3.6 28.9 - - + -
269B VAL* 4.4 9.2 - - + -
273B LEU* 4.1 16.2 - - + -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 4.4 0.2 + - - -
76B VAL* 1.3 78.0 - - - +
78B ILE* 1.3 57.6 + - - +
79B VAL* 4.2 1.3 - - + -
101B LEU* 3.3 20.9 - - + +
103B PHE* 4.1 14.1 - - + -
164B ILE* 4.2 17.3 - - + -
175B VAL* 4.5 9.9 - - + +
177B LEU 3.0 11.8 + - - +
178B VAL* 3.5 9.8 - - + -
179B LEU 2.7 31.9 + - - -
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 4.0 6.7 - - + +
77B ALA* 1.3 79.7 - - - +
79B VAL* 1.3 64.0 + - - +
80B GLY 3.5 21.1 + - - +
81B VAL* 5.4 3.7 - - + +
85B GLY 4.5 7.2 - - - +
88B THR* 4.4 9.4 - - + -
89B ALA* 3.7 36.8 - - + +
92B LEU* 4.4 4.0 - - + -
100B LEU* 4.1 20.6 - - + -
101B LEU 2.7 13.7 + - - +
102B LEU* 3.5 9.0 - - + +
103B PHE* 3.0 24.5 + - - +
179B LEU* 3.5 15.5 - - + -
181B CYS* 4.0 19.7 - - - -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA* 5.3 0.4 - - + -
78B ILE* 1.3 76.2 - - - +
80B GLY* 1.3 64.6 + - - +
103B PHE* 3.3 21.5 - - + +
104B ASP* 5.6 0.9 - - - -
151B ILE* 4.5 16.2 - - + -
160B PHE* 3.7 33.0 - - + -
178B VAL* 4.5 8.3 - - + -
179B LEU 2.8 13.8 + - - +
181B CYS* 2.9 28.6 + - - +
182B VAL* 3.7 12.4 + - + -
191B ILE* 3.8 29.4 - - + -
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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