Contacts of the strand formed by residues 147 - 152 (chain C) in PDB entry 4K2S
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 147 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C MET* 5.1 0.4 - - - -
121C THR 3.5 16.7 + - - +
122C TYR* 3.2 15.2 - - + -
123C ALA 3.1 18.4 + - - -
145C TYR* 3.3 7.1 + - - +
146C ARG* 1.3 83.2 - - + +
148C VAL* 1.3 67.4 + - - +
208C LEU* 4.4 0.2 - - - -
209C HIS* 3.2 26.0 - - + -
211C LEU* 4.1 2.5 - - + -
340C ILE* 3.8 12.8 - - + -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 4.6 0.4 - - - -
123C ALA* 3.4 6.1 - - + +
125C CYS* 3.6 28.7 - - - -
137C VAL* 4.3 11.4 - - + +
140C HIS* 4.2 15.3 - - + -
141C VAL* 5.0 1.8 - - + -
145C TYR* 4.6 5.2 - - + -
147C ALA* 1.3 80.9 - - - +
149C ARG* 1.3 61.6 + - - +
150C VAL* 3.9 16.1 + - + -
200C VAL* 5.4 0.2 - - + -
208C LEU* 3.7 34.8 - - + -
209C HIS 2.9 9.9 + - - +
210C VAL* 3.4 5.1 - - + +
211C LEU* 2.9 27.4 + - - +
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Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 3.7 32.1 + - + -
123C ALA 2.8 12.1 + - - +
124C HIS* 3.2 38.4 + - + +
125C CYS* 2.8 33.3 + - - +
126C THR* 6.2 0.4 - - - -
148C VAL* 1.3 74.1 - - - +
150C VAL* 1.3 61.2 + - - +
151C GLN* 3.5 28.4 + - - +
161C TYR* 2.3 45.3 + - - -
162C GLY* 4.3 8.3 + - - -
211C LEU* 3.3 19.3 - - + +
212C HIS* 4.2 0.9 - - - +
213C ASP* 3.1 22.5 + - - +
239C GLU* 4.7 5.6 + - - +
286C ARG* 6.1 0.6 - - - +
342C GLU* 4.8 2.4 + - - -
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C CYS* 3.4 2.9 - - + -
133C CYS* 3.8 11.2 - - - -
137C VAL* 3.7 30.1 - - + -
148C VAL* 4.0 15.3 - - + +
149C ARG* 1.3 77.4 - - - +
151C GLN* 1.3 66.7 + - - +
196C LEU* 3.8 9.5 - - + +
197C PHE* 3.7 27.6 - - + -
200C VAL* 4.2 10.8 - - + -
210C VAL* 3.8 18.6 - - + -
211C LEU 2.9 10.3 + - - +
212C HIS* 2.8 26.7 + - - -
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Residues in contact with GLN 151 (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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125C CYS 3.1 8.4 + - - +
126C THR* 3.4 22.0 - - - -
127C GLY 3.4 1.9 + - - -
133C CYS* 3.5 4.9 - - - -
149C ARG* 3.5 36.0 - - - +
150C VAL* 1.3 87.2 - - - +
152C SER* 1.3 62.8 + - - +
161C TYR* 3.7 26.2 + - - +
162C GLY 3.9 18.4 - - - +
163C VAL* 4.0 1.3 - - - -
189C TYR* 6.0 0.2 - - - -
196C LEU* 3.9 4.9 - - - -
212C HIS* 3.3 15.2 - - - -
213C ASP* 2.8 45.9 + - - +
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Residues in contact with SER 152 (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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127C GLY 3.2 12.3 - - - -
129C THR 3.9 19.5 - - - -
130C ILE* 3.9 7.4 - - - +
133C CYS* 4.3 5.8 - - - -
151C GLN* 1.3 76.2 - - - +
153C GLY* 1.3 72.0 + - - +
154C VAL* 4.5 4.7 - - - +
160C THR* 3.5 10.4 + - - +
163C VAL* 3.4 6.3 - - - -
189C TYR* 6.1 0.2 - - - -
192C HIS* 3.8 15.2 + - - -
196C LEU* 3.8 21.3 - - - +
212C HIS* 5.6 0.8 - - - -
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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
------------------------------------------------------------
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