Contacts of the strand formed by residues 125 - 130 (chain C) in PDB entry 3O4O
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 TYR 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A HIS* 3.9 11.0 - - + -
31A LEU 3.6 17.0 - - - +
32A GLN* 3.5 31.0 - - + -
27C ARG* 3.0 21.9 + - - -
123C ILE* 3.8 6.1 - - + -
124C SER* 1.3 74.3 - - - +
126C PRO* 1.3 67.1 - - + +
127C GLN* 3.3 9.1 + - - +
140C PRO* 3.3 42.8 - - + -
141C ASP* 2.6 31.8 + - - +
209C ARG* 3.8 16.9 + - + -
210C SER 2.7 21.9 + - - +
211C ILE* 3.7 7.3 - - + -
212C GLU 2.9 23.5 + - - -
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Residues in contact with PRO 126 (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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11A ARG* 3.1 22.3 + - - -
31A LEU 3.7 17.4 - - - +
33A GLY* 3.8 11.7 - - - -
36A MET* 3.6 28.3 - - + -
124C SER* 3.5 8.5 - - - +
125C TYR* 1.3 80.1 - - - +
127C GLN* 1.3 64.2 + - - +
128C ILE* 5.1 2.9 - - + -
212C GLU* 3.5 13.2 - - + +
214C ARG* 3.7 30.1 - - - +
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Residues in contact with GLN 127 (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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15A GLN* 3.1 37.0 + - - +
30A HIS* 3.9 15.2 - - - -
125C TYR* 3.7 8.9 - - - +
126C PRO* 1.3 76.1 + - - +
128C ILE* 1.3 59.8 + - - +
129C LEU* 4.5 0.7 - - - -
137C LEU* 3.6 19.7 - - + -
138C VAL 3.1 35.4 + - - -
140C PRO* 4.2 4.0 - - - +
211C ILE* 3.2 35.7 - - + +
212C GLU 2.9 6.4 + - - +
213C LEU* 3.2 6.1 - - - +
214C ARG* 2.9 24.7 + - - +
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Residues in contact with ILE 128 (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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11A ARG* 3.6 21.1 - - - +
15A GLN* 2.7 35.4 + - - -
147A THR* 6.5 1.8 - - + -
149A GLN* 4.4 28.0 - - + +
126C PRO* 5.0 3.1 - - + +
127C GLN* 1.3 76.2 - - - +
129C LEU* 1.3 72.3 + - - +
130C THR 4.8 0.4 - - - +
214C ARG* 3.4 22.0 - - + +
216C LYS* 3.4 43.5 - - + +
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Residues in contact with LEU 129 (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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15A GLN* 3.6 9.4 - - - +
128C ILE* 1.3 98.4 - - - +
130C THR* 1.3 67.2 + - - +
133C THR* 5.6 0.2 - - - +
134C SER 4.8 0.7 - - - -
135C GLY* 3.2 42.8 - - - +
136C VAL* 3.7 2.9 - - - +
137C LEU* 3.5 29.4 - - + -
181C VAL* 4.3 18.8 - - + -
184C VAL* 4.8 12.1 - - + -
213C LEU* 3.6 15.5 - - + -
214C ARG 2.8 6.7 + - - -
215C ILE* 3.0 11.3 - - - +
216C LYS 3.0 19.1 + - - -
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Residues in contact with THR 130 (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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108A ASN* 5.5 11.7 - - + +
109A LYS* 5.6 7.6 - - - +
147A THR* 5.8 4.3 - - - +
128C ILE* 4.8 0.8 - - - +
129C LEU* 1.3 73.3 - - - +
131C LEU* 1.3 59.4 + - - +
133C THR* 2.6 33.0 + - + +
184C VAL* 3.1 9.5 - - - +
216C LYS* 3.1 21.8 + - - +
217C LYS 5.0 0.7 - - - -
218C LYS* 3.3 39.3 + - - +
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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