Contacts of the strand formed by residues 254 - 260 (chain A) in PDB entry 4Z2C
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 GLU 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 ILE* 4.2 14.1 - - + +
247A GLU 3.7 5.6 - - - +
248A THR* 4.9 3.1 - - - +
249A THR* 4.4 2.9 - - - +
253A ARG* 1.3 79.0 - - - +
255A ARG* 1.3 60.5 + - - +
303A GLU* 4.2 1.0 - - - +
304A VAL* 3.2 33.9 + - + +
305A LYS 5.4 1.2 + - - +
308A ALA 3.3 12.9 - - - +
309A SER* 3.7 2.8 - - - -
310A ALA* 2.8 46.9 + - + +
311A ASN* 4.5 10.9 + - - -
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Residues in contact with ARG 255 (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 GLU 3.7 0.2 - - - +
246A ILE* 3.3 7.1 - - - +
247A GLU* 2.7 64.3 + - - +
248A THR 4.7 0.6 + - - -
249A THR* 3.3 39.6 - - + +
250A LYS 4.8 0.8 - - - +
254A GLU* 1.3 77.8 - - - +
256A ILE* 1.3 63.4 + - - +
257A VAL* 3.7 22.8 + - + -
292A GLU* 4.9 6.1 + - - -
299A ARG* 3.9 9.5 - - - +
301A VAL* 3.6 26.3 - - + +
302A ILE 4.0 3.8 - - - -
303A GLU* 2.3 37.3 + - + +
304A VAL 4.7 0.2 - - - +
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Residues in contact with ILE 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 THR* 4.9 1.8 - - + -
245A GLU 3.8 3.1 - - - +
246A ILE* 3.8 17.3 - - + -
255A ARG* 1.3 73.4 - - - +
257A VAL* 1.3 63.4 + - - +
258A VAL* 4.3 17.7 - - + -
300A PHE 3.4 1.2 - - - +
301A VAL* 3.4 6.1 - - - +
302A ILE* 2.9 51.4 + - + +
304A VAL* 4.5 3.6 - - + -
310A ALA* 3.3 32.8 - - + +
313A ILE* 3.9 15.7 - - + -
314A LEU* 3.7 38.8 - - + +
317A LEU* 4.7 7.6 - - + -
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Residues in contact with VAL 257 (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 THR* 3.2 4.3 - - - -
245A GLU* 2.8 47.9 + - + +
247A GLU* 3.7 25.8 - - + +
255A ARG* 3.7 27.4 - - + +
256A ILE* 1.3 75.8 - - - +
258A VAL* 1.3 63.5 + - - +
259A THR* 3.5 18.8 + - + +
299A ARG* 3.8 35.7 - - + +
300A PHE 3.5 3.4 - - - +
301A VAL* 4.8 2.0 - - + -
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Residues in contact with VAL 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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242A SER* 3.7 20.2 - - - -
243A ARG 4.0 1.1 - - - +
244A THR* 3.7 26.9 - - + -
256A ILE* 4.3 10.1 - - + -
257A VAL* 1.3 71.2 - - - +
259A THR* 1.3 61.6 + - - +
260A GLU 4.1 1.3 - - - +
261A PHE* 3.5 26.0 - - + -
298A VAL* 3.9 2.9 - - - +
299A ARG* 3.8 2.6 - - - -
300A PHE* 2.8 64.6 + - + +
302A ILE* 6.0 1.8 - - + +
317A LEU* 6.1 0.2 - - + -
323A MET* 3.8 20.0 - - + -
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Residues in contact with THR 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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243A ARG* 2.8 37.4 + - - +
244A THR* 4.6 1.2 - - - -
245A GLU* 4.6 15.5 + - - +
257A VAL* 3.5 22.6 + - + +
258A VAL* 1.3 77.2 - - - +
260A GLU* 1.3 68.0 + - - +
298A VAL* 3.3 41.2 + - - +
299A ARG* 5.2 1.1 - - + -
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Residues in contact with GLU 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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217A THR* 3.3 17.7 - - - +
218A GLY* 3.3 5.0 - - - -
219A ALA* 2.4 40.5 + - - +
242A SER* 3.0 10.4 - - - -
243A ARG* 2.9 69.0 + - + -
258A VAL* 3.7 0.6 - - - -
259A THR* 1.3 87.5 - - - +
261A PHE* 1.3 63.8 + - - +
298A VAL* 5.3 0.2 - - - -
481A ARG* 4.2 3.9 - - - +
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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