Contacts of the strand formed by residues 5 - 10 (chain C) in PDB entry 2RA2
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 ASN 5 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLY 3.7 6.1 + - - -
4C PRO* 1.3 82.1 + - - +
6C TYR* 1.3 58.5 + - - +
17C VAL* 4.4 5.7 - - + +
18C THR 3.2 18.2 + - - +
19C ASP* 3.7 11.4 + - - +
20C GLY 3.7 7.9 - - - +
53C ALA* 3.4 8.1 - - - +
54C LEU* 2.7 52.2 + - + +
55C GLU 4.5 1.0 + - - -
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Residues in contact with TYR 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 3.6 34.2 - - + +
5C ASN* 1.3 79.4 - - - +
7C VAL* 1.3 61.0 + - - +
8C MSE 4.2 0.4 - - - -
16C ILE 3.8 0.2 - - - +
17C VAL* 3.2 5.5 - - - +
18C THR* 2.7 45.0 + - + +
20C GLY 3.9 1.1 - - - -
21C LYS* 3.5 49.5 - - + +
22C PRO* 4.2 6.3 - - + -
51C MSE 4.2 22.4 - - + -
52C VAL* 3.4 9.9 - - - +
53C ALA* 3.6 29.3 - - + +
54C LEU* 3.7 4.7 - - - +
42D GLN* 4.6 10.5 - - - -
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Residues in contact with VAL 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 1.3 75.5 - - - +
8C MSE 1.3 67.3 + - - +
9C HIS* 3.9 26.2 + - + +
15C SER* 4.3 12.6 - - - -
16C ILE 3.3 10.3 - - - +
17C VAL* 4.9 2.2 - - + +
51C MSE 3.4 4.1 - - - -
52C VAL* 2.9 51.7 + - + +
54C LEU* 4.5 19.1 - - + -
57C LEU* 3.8 24.5 - - + -
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Residues in contact with MSE 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 1.3 73.0 - - - +
9C HIS* 1.3 61.9 + - - +
10C THR* 3.8 3.4 + - + -
14C ARG 3.5 3.6 - - - +
15C SER* 3.5 1.2 - - - -
16C ILE* 2.8 53.1 + - + +
18C THR* 3.7 22.4 - - + -
22C PRO* 4.2 10.5 - - - -
31C ILE* 4.4 13.9 - - - -
33C TYR* 3.7 38.4 - - + -
43C ILE* 4.5 5.4 - - + -
48C VAL* 4.2 21.8 - - + -
50C GLU 3.5 4.9 - - - -
51C MSE 3.8 36.3 - - + -
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Residues in contact with HIS 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.9 24.8 - - + +
8C MSE 1.3 71.2 - - - +
10C THR* 1.3 63.1 + - - +
14C ARG 3.4 4.8 + - - +
15C SER* 3.2 26.7 + - - -
48C VAL* 3.9 1.6 - - - -
49C LYS* 2.9 27.7 + - + +
50C GLU* 2.9 50.3 + - + +
51C MSE 5.4 0.2 - - - -
52C VAL* 5.1 5.9 - - + +
57C LEU* 3.9 28.2 - - + +
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Residues in contact with THR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C MSE 4.5 5.6 - - + +
9C HIS* 1.3 78.5 - - - +
11C ASN* 1.3 65.6 + - - +
12C ASP* 2.6 27.4 + - - -
13C GLY* 3.5 9.2 + - - -
14C ARG* 2.9 30.3 + - + +
16C ILE* 3.9 28.5 - - + -
43C ILE* 3.9 14.8 - - + -
47C ASP* 3.1 18.8 - - - +
48C VAL* 4.4 2.0 - - + +
49C LYS* 4.5 5.8 - - - +
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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