Contacts of the helix formed by residues 32 - 38 (chain S) in PDB entry 2FRV
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 32 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200L LEU* 3.8 37.7 - - + +
24S VAL* 4.4 8.5 - - + +
25S LEU* 4.1 39.2 + - + +
27S THR* 3.6 17.5 + - + +
31S TYR* 1.3 71.7 - - - +
33S ASP* 1.3 61.4 + - - +
35S LEU* 3.4 8.2 - - + +
36S ILE* 3.0 51.3 + - + +
48S LEU* 6.4 0.9 - - + -
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Residues in contact with ASP 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157L LYS* 5.7 5.3 + - - +
197L LEU* 4.6 17.9 - - + +
200L LEU* 4.3 23.2 - - + +
201L ARG* 2.7 47.6 + - - +
31S TYR* 3.2 9.3 - - - +
32S VAL* 1.3 80.3 + - - +
34S GLU* 1.3 68.5 + - - +
36S ILE* 4.7 4.3 - - - -
37S LEU* 2.9 45.0 + - + +
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Residues in contact with GLU 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L ARG* 3.9 6.6 + - - +
29S ASP* 4.7 2.9 - - - +
30S PRO* 3.2 21.0 - - + +
31S TYR* 3.0 43.0 + - - +
33S ASP* 1.3 88.2 + - - +
35S LEU* 1.3 55.6 + - - +
37S LEU* 5.1 0.2 - - - -
38S ASP* 2.7 46.8 + - + +
39S VAL* 3.1 11.1 + - + +
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Residues in contact with LEU 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S VAL* 4.5 16.6 - - + -
27S THR* 4.6 4.3 - - + -
30S PRO* 4.4 7.3 - - + +
31S TYR 3.2 12.8 + - - +
32S VAL* 3.4 14.1 - - + +
33S ASP 3.2 0.2 - - - -
34S GLU* 1.3 75.3 - - - +
36S ILE* 1.3 75.4 + - + +
39S VAL* 2.9 32.8 + - + -
40S ILE* 2.9 48.0 + - + +
42S MET* 5.9 0.9 - - + -
155S PHE* 5.6 3.8 - - + -
156S VAL* 4.4 36.3 - - + -
159S VAL* 5.1 8.1 - - + -
160S VAL* 5.1 1.3 - - + -
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Residues in contact with ILE 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L LEU* 5.1 0.9 - - - +
169L ILE* 5.4 12.8 - - + -
200L LEU* 6.3 2.5 - - + -
6S ARG* 3.1 18.5 + - - -
24S VAL* 6.1 0.4 - - + -
32S VAL* 3.0 27.3 + - + +
33S ASP* 4.6 3.4 - - - +
35S LEU* 1.3 102.6 - - + +
37S LEU* 1.3 72.4 + - + +
40S ILE* 3.3 19.9 - - + +
42S MET* 4.1 33.2 + - + +
48S LEU* 6.4 2.2 - - + -
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Residues in contact with LEU 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L LYS* 4.5 26.7 - - + +
161L LEU* 4.1 33.7 - - + +
170L PHE* 5.9 4.5 - - + -
197L LEU* 4.5 21.8 - - + -
6S ARG* 4.0 18.1 + - - +
33S ASP* 2.9 25.4 + - + +
36S ILE* 1.3 90.6 - - + +
38S ASP* 1.3 74.2 + - - +
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Residues in contact with ASP 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S ARG* 3.7 14.9 - - - +
34S GLU* 2.7 35.9 + - + +
35S LEU 3.6 0.2 + - - -
37S LEU* 1.3 95.1 - - - +
39S VAL* 1.3 64.3 + - + +
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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