Contacts of the strand formed by residues 258 - 262 (chain A) in PDB entry 4C1Q
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 LEU 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A ILE* 4.0 22.0 - - + -
249A SER* 3.8 5.6 - - - -
250A PRO* 3.7 24.2 - - + -
251A SER 3.9 0.2 - - - -
257A GLY* 1.3 74.8 - - - -
259A GLY* 1.3 59.4 + - - +
318A TYR* 3.6 21.6 - - + +
320A ASN* 2.9 16.9 + - - -
394A SAH 3.2 23.4 + - - +
199B ASP* 5.7 1.3 - - - +
201B ASP* 3.7 39.0 - - + +
202B TYR* 3.8 23.8 - - + +
213B ILE* 3.9 18.6 - - + -
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Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG 3.7 0.2 - - - +
248A ILE* 3.3 9.0 - - - +
249A SER 2.8 34.3 + - - +
251A SER* 3.8 1.9 - - - +
258A LEU* 1.3 75.1 - - - +
260A VAL* 1.3 64.9 + - - -
261A TRP* 4.1 3.1 - - - -
318A TYR* 3.4 11.4 - - - -
320A ASN* 3.5 11.4 - - - -
352A GLU* 3.8 8.1 - - - -
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.9 23.6 - - + -
246A LEU* 4.2 5.6 - - + -
247A ARG 3.5 5.8 - - - +
248A ILE* 4.3 6.1 - - + -
259A GLY* 1.3 76.2 - - - +
261A TRP* 1.3 64.1 + - - +
315A TRP* 4.0 19.7 - - + +
318A TYR* 3.7 23.8 + - + -
319A VAL* 3.7 29.6 - - + +
352A GLU* 3.4 7.4 - - - +
353A LEU* 2.7 44.1 + - + +
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Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LEU* 3.3 9.2 - - - +
247A ARG* 2.9 40.8 + - + +
249A SER* 3.4 28.0 + - - -
250A PRO 3.2 21.0 + - - -
251A SER* 4.4 1.2 - - - +
252A GLY* 3.4 33.4 - - - -
259A GLY 3.9 3.6 + - - -
260A VAL* 1.3 78.1 - - - +
262A ASN* 1.3 62.3 + - - +
263A GLU* 3.7 17.0 - - - +
350A GLY* 3.3 30.7 - - - -
351A CYS 3.6 4.0 - - - -
352A GLU* 3.5 31.4 - - + +
353A LEU* 4.8 0.9 - - - -
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Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A GLY 3.6 8.1 - - - +
246A LEU* 3.6 12.4 - - + +
261A TRP* 1.3 74.2 - - - +
263A GLU* 1.3 64.4 + - - +
264A ALA* 4.1 1.7 + - - +
265A SER 2.8 29.8 + - - +
267A LEU* 3.7 20.5 - - + +
347A ILE* 3.1 29.8 + - + -
348A ARG 3.4 16.8 + - - +
349A PRO* 3.6 2.2 - - - +
350A GLY* 2.8 31.5 + - - -
351A CYS 2.9 16.3 + - - +
353A LEU* 4.2 4.7 - - + +
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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