Contacts of the strand formed by residues 254 - 258 (chain A) in PDB entry 6N8P
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 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A VAL* 3.9 12.3 - - + -
247A SER 3.1 14.4 - - - +
248A CYS* 4.0 5.2 - - + -
249A HIS* 4.5 1.6 - - - -
253A SER* 1.3 76.2 - - - +
255A CYS* 1.3 65.4 + - - +
256A GLN* 4.8 15.0 - - + -
270A ARG 5.8 0.4 - - - -
271A SER* 4.7 1.1 - - - -
272A LEU* 3.1 56.9 + - + +
274A PRO* 3.5 33.7 - - + -
283A ILE* 4.3 6.5 - - + -
286A ILE* 3.5 28.0 - - + -
288A TRP* 5.5 1.5 - + - -
298A THR* 3.8 29.8 + - + +
300A PHE* 4.5 6.1 - + - -
318A ILE* 4.2 9.9 - - - +
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Residues in contact with CYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 3.4 4.8 - - - +
247A SER* 3.0 32.3 + - - +
249A HIS* 3.5 22.0 - - - -
254A TYR* 1.3 74.8 - - - +
256A GLN* 1.3 62.6 + - - +
257A TRP* 2.9 44.6 - - - -
268A PRO* 4.5 9.0 - - + -
270A ARG 3.1 15.5 - - - +
271A SER* 3.7 18.2 - - - +
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Residues in contact with GLN 256 (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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244A LEU* 3.9 20.5 - - + +
245A LEU 3.2 4.3 - - - +
246A VAL* 4.1 16.4 - - + -
254A TYR* 4.8 11.7 - - + -
255A CYS* 1.3 79.0 - - - +
257A TRP* 1.3 61.8 + - - +
268A PRO* 3.8 1.6 - - - +
269A LEU* 2.8 55.8 + - + +
270A ARG* 3.1 29.6 + - - +
288A TRP* 3.5 36.0 - - - -
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Residues in contact with TRP 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 3.6 15.5 - - - +
227A PHE* 3.3 57.4 - + + -
228A LEU 3.8 13.9 - - - -
229A SER* 4.4 11.0 - - - -
230A SER 5.6 1.3 - - - -
244A LEU* 3.2 6.9 - - - +
245A LEU* 2.6 55.7 + - + +
247A SER* 2.9 27.9 + - - -
255A CYS* 2.9 27.1 - - - -
256A GLN* 1.3 76.9 - - - +
258A PRO* 1.3 65.9 - - + +
266A PRO* 4.1 4.5 - - + -
267A GLU* 3.8 9.9 - - - -
268A PRO* 3.4 44.2 - - + -
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Residues in contact with PRO 258 (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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225A TYR* 2.8 23.2 + - - -
243A ARG 3.9 8.3 - - - +
244A LEU* 4.2 3.8 - - + -
257A TRP* 1.3 84.9 - - + +
259A VAL* 1.3 60.7 + - - +
260A SER* 4.0 3.7 + - - -
263A ALA 5.1 0.5 - - - +
266A PRO* 3.7 17.9 - - + +
267A GLU 4.1 13.5 - - - +
269A LEU* 4.1 30.7 - - + -
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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