Contacts of the strand formed by residues 78 - 82 (chain C) in PDB entry 2F4N
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.2 13.7 - - + -
14C ILE 2.9 11.3 + - - +
15C ILE* 3.2 23.5 - - + -
16C THR 2.9 23.2 + - - -
77C SER* 1.3 77.5 - - - +
79C HIS* 1.3 76.2 + - - +
80C VAL* 4.6 0.9 - - + -
103C TYR* 3.5 11.7 - - + +
105C VAL* 4.3 18.4 - - + -
148C GLY* 4.3 12.6 - - - +
151C ILE* 3.9 26.0 - - + -
152C LEU* 4.3 15.5 - - + -
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Residues in contact with HIS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 2.4 47.0 + - + +
67C LEU* 5.6 1.3 - - + -
71C ILE* 3.5 46.6 - - + +
74C PHE* 4.1 11.4 - + - -
77C SER* 3.3 33.8 + - - -
78C VAL* 1.3 77.7 + - - +
80C VAL* 1.3 60.1 + - - +
81C ALA 3.8 0.5 + - - -
102C TYR* 3.9 13.6 - + - -
103C TYR 2.8 16.1 + - - +
104C LEU* 3.6 10.9 - - + -
105C VAL 2.7 32.3 + - - +
112C PHE* 3.8 5.0 - - + -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 4.1 25.1 - - + -
16C THR* 2.9 11.9 + - - +
17C LEU* 3.4 18.8 - - + -
18C THR* 3.0 23.9 + - - +
19C THR* 5.5 0.2 - - - +
31C MSE 4.9 5.2 - - - -
35C ILE* 5.5 0.2 - - + -
67C LEU* 6.0 0.4 - - - -
78C VAL* 4.6 1.1 - - + -
79C HIS* 1.3 75.8 - - - +
81C ALA* 1.3 61.6 + - - +
82C VAL* 3.8 13.0 - - + +
105C VAL* 3.4 15.9 - - + +
144C TYR* 3.7 46.0 - - + +
145C ALA* 4.7 3.1 - - - +
148C GLY* 4.2 4.9 - - - -
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C THR* 3.3 10.3 - - - +
67C LEU* 3.7 18.6 - - + -
79C HIS 3.8 0.6 + - - -
80C VAL* 1.3 73.8 - - - +
82C VAL* 1.3 62.5 + - - +
83C ILE* 4.0 2.5 - - + -
105C VAL 3.0 5.9 + - - -
106C GLY* 3.5 8.0 - - - -
107C PRO* 3.4 21.3 - - - +
111C LEU* 3.2 25.5 - - + +
112C PHE* 3.5 18.2 - - + -
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C THR 2.9 9.1 + - - -
19C THR* 3.8 12.7 - - + -
20C ASP* 3.5 13.2 - - - +
21C PHE* 3.5 28.9 - - + -
31C MSE 4.5 15.3 - - + -
80C VAL* 3.8 22.4 - - + -
81C ALA* 1.3 76.8 - - - +
83C ILE* 1.3 68.4 + - - +
84C ASP 5.8 0.4 - - - +
107C PRO* 4.6 3.1 - - + -
140C GLY 5.9 0.2 - - - -
141C ARG* 5.4 3.4 - - - -
144C TYR* 3.9 30.7 - - + -
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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
------------------------------------------------------------
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