Contacts of the strand formed by residues 255 - 259 (chain A) in PDB entry 5G04
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 ILE 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PHE* 3.5 25.7 - - + +
249A LEU* 3.6 19.5 - - - +
250A ASN* 3.8 17.0 + - + +
253A PRO* 3.1 40.8 + - + +
254A SER* 1.3 76.5 + - - +
256A VAL* 1.3 82.6 + - - +
257A MET* 5.1 0.9 - - - -
268A VAL* 3.9 15.3 - - + -
269A TRP 3.2 11.0 - - - +
270A THR* 4.2 2.0 - - + +
271A LEU* 4.3 0.6 - - - +
432A ILE* 4.1 7.6 - - + -
442A LEU* 3.7 24.5 - - + -
457A PHE* 6.1 1.1 - - + -
466A LEU* 5.0 12.3 - - + -
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Residues in contact with VAL 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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188A LEU* 5.1 0.9 - - + -
210A MET* 5.2 3.6 - - + -
223A LEU* 5.6 2.2 - - + -
246A ILE* 3.7 27.8 - - + -
248A PHE 3.4 4.7 - - - -
249A LEU* 4.3 0.2 - - + -
255A ILE* 1.3 79.4 - - - +
257A MET* 1.3 63.3 + - - +
258A THR* 4.1 15.5 - - + -
267A SER 3.4 3.8 - - - +
268A VAL* 3.4 4.7 - - - -
269A TRP* 2.8 51.2 + - + -
271A LEU* 3.3 34.1 - - + +
409A ILE* 4.0 19.3 - - + -
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Residues in contact with MET 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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245A LYS 3.4 0.2 - - - +
246A ILE 3.5 0.5 - - - -
247A VAL* 2.6 49.9 + - + +
248A PHE* 3.0 37.9 + - + +
255A ILE* 5.1 0.7 - - - -
256A VAL* 1.3 79.4 - - - +
258A THR* 1.3 58.9 + - - +
266A HIS* 3.8 25.1 - - + -
267A SER 3.5 9.6 - - - +
268A VAL* 3.7 27.6 - - + -
413A TRP 5.4 0.2 - - - +
427A ALA* 5.5 0.2 - - + -
430A VAL* 3.6 16.2 - - + -
442A LEU* 4.6 5.4 - - - -
444A PHE* 3.5 36.8 - - + -
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Residues in contact with THR 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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210A MET* 4.8 8.7 - - + -
244A MET* 4.4 17.2 - - + +
245A LYS 3.0 18.4 - - - +
246A ILE* 4.6 1.6 - - - +
247A VAL* 4.8 2.1 - - - +
256A VAL* 4.1 13.5 - - + -
257A MET* 1.3 77.9 - - - +
259A TYR* 1.3 62.1 + - - +
260A ASP* 4.5 4.5 + - - +
265A VAL 3.6 0.2 - - - +
266A HIS* 3.4 12.9 + - - +
267A SER* 3.1 42.7 + - - -
269A TRP* 3.2 33.7 + - + +
409A ILE* 5.9 1.8 - - + -
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Residues in contact with TYR 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 ALA 2.8 19.9 - - - +
244A MET* 4.2 1.6 - - - -
245A LYS* 2.9 18.5 + - + +
247A VAL* 5.4 1.6 - - + -
258A THR* 1.3 72.9 - - - +
260A ASP* 1.3 68.6 + - - +
261A ALA* 3.7 13.2 + - + -
263A GLN 5.0 0.6 + - - -
264A ASN 2.8 30.6 + - - -
265A VAL 3.9 5.6 - - - -
266A HIS* 3.8 18.6 - + + +
425A SER* 3.1 45.1 + - - -
426A GLN* 3.5 55.9 - - + +
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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