Contacts of the strand formed by residues 12 - 16 (chain C) in PDB entry 1RFO
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 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.4 18.2 - - + -
16A LYS* 3.2 14.4 - - + +
26A PHE* 3.3 40.5 - - + -
10C GLY 4.1 1.0 + - - -
11C GLN* 1.3 72.9 - - - +
13C TYR* 1.3 56.2 + - - +
22C LEU* 2.7 29.2 - - + +
23C LEU* 2.7 18.7 + - + -
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Residues in contact with TYR 13 (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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14A VAL* 3.2 7.9 - - - +
15A ARG* 2.5 53.6 + - - +
6C ALA* 3.8 1.8 - - + -
7C PRO* 3.3 44.5 - - + +
9C ASP* 4.1 2.8 + - - -
11C GLN* 3.4 45.5 + - + -
12C ALA* 1.3 73.1 - - - +
14C VAL* 1.3 64.1 + - - +
20C TRP* 3.1 52.0 - - + -
21C VAL 3.0 12.3 - - - -
22C LEU* 3.3 17.9 - - + +
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Residues in contact with VAL 14 (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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14A VAL* 4.6 2.9 - - + +
12B ALA* 3.4 20.9 - - + -
13B TYR 3.0 21.5 - - - +
14B VAL* 4.4 3.8 - - + +
23B LEU* 3.1 45.5 - - + -
13C TYR* 1.3 78.2 - - - +
15C ARG* 1.3 60.7 + - - +
16C LYS 3.5 0.9 + - - -
19C GLU 3.2 5.2 - - - +
20C TRP* 3.3 6.0 - - - -
21C VAL* 2.5 44.7 + - + +
22C LEU 3.8 0.9 - - - -
23C LEU* 3.4 18.8 - - + -
26C PHE* 3.8 4.3 - - + -
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Residues in contact with ARG 15 (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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5B GLU* 2.3 35.1 + - - -
6B ALA* 4.1 8.8 - - + +
8B ARG* 4.4 0.8 - - - +
13B TYR* 2.5 46.0 + - - +
20B TRP* 3.7 20.6 - - + -
3C ILE* 3.0 22.8 - - + +
4C PRO* 3.1 25.3 - - - +
14C VAL* 1.3 71.6 - - - +
16C LYS* 1.3 56.2 + - - +
18C GLY* 2.6 36.6 + - - +
19C GLU* 3.1 14.5 - - - +
20C TRP* 3.0 60.9 - - + +
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Residues in contact with LYS 16 (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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7B PRO 4.7 2.2 - - - -
10B GLY* 2.9 30.1 - - - +
11B GLN 2.7 28.7 - - - +
12B ALA* 3.3 13.0 - - + +
14C VAL 3.5 0.2 + - - -
15C ARG* 1.3 73.1 - - - +
17C ASP* 1.3 79.0 + - + +
18C GLY 3.2 1.1 - - - -
19C GLU* 3.0 23.4 + - - +
21C VAL* 3.7 29.5 - - + +
26C PHE* 4.6 7.0 - - + -
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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