Contacts of the strand formed by residues 251 - 257 (chain A) in PDB entry 3KQG
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.9 28.2 - + + +
210A SER 4.0 9.0 + - - -
245A THR 5.2 0.2 + - - -
246A ALA* 3.4 37.9 + - + -
249A LEU* 3.4 36.0 - - + +
250A ILE* 1.3 74.5 - - - +
252A TRP* 1.3 60.6 + - - +
253A ILE* 4.1 0.2 - - - +
297A ASN* 3.1 5.1 - - - +
298A ILE* 2.7 40.6 + - + +
316A LEU* 3.0 35.2 - - + +
317A PHE 3.6 7.6 - - - -
318A ILE* 3.5 37.0 - - + -
211C LEU* 4.2 9.2 - - - +
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Residues in contact with TRP 252 (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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214A LYS 2.8 29.0 + - - -
215A THR 4.1 2.5 - - - -
216A TRP* 3.4 28.1 - + + +
219A ALA* 4.3 5.6 - - + -
230A LEU* 4.0 8.4 - - + +
251A TYR* 1.3 74.1 - - - +
253A ILE* 1.3 62.1 + - - +
295A CYS* 3.5 31.0 - - + -
296A GLY 3.4 22.7 - - - -
297A ASN* 3.8 14.5 - - + +
309A ALA* 4.0 11.4 - - + -
310A PRO 3.3 24.5 - - - -
311A CYS* 4.0 7.0 - - - -
313A LYS 3.2 19.8 + - - -
315A PHE* 3.5 35.8 - + + +
316A LEU 2.7 8.5 + - - -
317A PHE* 3.8 11.2 - - + +
318A ILE* 3.1 23.7 + - - +
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Residues in contact with ILE 253 (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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216A TRP* 2.9 24.3 + - - -
230A LEU* 3.5 11.8 - - - +
231A THR* 3.6 26.7 - - + +
233A VAL* 4.3 6.1 - - + -
242A LEU* 5.2 0.4 - - + -
251A TYR 4.1 6.3 - - - +
252A TRP* 1.3 79.5 - - - +
254A GLY* 1.3 60.0 + - - +
255A LEU* 3.1 22.2 + - + +
266A TRP* 4.2 8.7 - - + -
296A GLY 3.1 20.1 + - - +
297A ASN* 4.2 1.3 - - - -
298A ILE* 4.3 20.4 - - + +
306A TRP* 3.7 34.3 - - + +
318A ILE* 4.3 9.4 - - + -
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Residues in contact with GLY 254 (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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216A TRP* 4.2 3.1 - - - -
230A LEU* 3.5 22.2 - - - +
231A THR 2.7 23.1 + - - -
253A ILE* 1.3 70.2 - - - +
255A LEU* 1.3 62.9 + - - +
256A THR* 3.4 1.4 + - - +
265A SER 3.3 4.3 - - - +
266A TRP* 3.4 8.8 - - - -
267A VAL* 3.0 32.0 + - - +
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Residues in contact with LEU 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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216A TRP* 3.3 14.0 + - - -
253A ILE* 3.1 11.0 + - + -
254A GLY* 1.3 74.9 - - - +
256A THR* 1.3 58.0 + - - +
264A TRP* 3.8 13.7 - - + -
265A SER 3.7 2.9 - - - +
266A TRP* 3.5 24.6 - - + -
272A PHE* 3.4 34.5 - - + -
281A TRP* 4.0 16.4 - - + -
295A CYS* 3.6 1.2 - - - -
296A GLY* 3.1 38.5 + - - +
306A TRP* 3.5 39.9 - - + -
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Residues in contact with THR 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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216A TRP* 3.7 26.4 - - + -
217A TYR* 5.4 4.2 + - - -
254A GLY 4.0 4.9 - - - +
255A LEU* 1.3 76.7 - - - +
257A LYS* 1.3 64.4 + - - +
258A ALA 4.1 0.2 + - - -
263A ASP 3.7 0.3 - - - +
264A TRP* 3.4 7.1 - - - -
265A SER* 2.8 63.8 + - - +
266A TRP 4.5 0.2 - - - -
267A VAL* 4.3 10.3 - - + +
294A HIS 3.7 9.8 + - - -
295A CYS* 4.8 1.9 - - - -
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Residues in contact with LYS 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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256A THR* 1.3 79.1 + - - +
258A ALA* 1.3 58.9 + - - +
259A GLY 2.8 17.2 + - - +
260A MET* 4.3 1.0 - - - +
261A GLU* 3.0 32.3 - - - +
262A GLY 2.8 35.5 + - - +
263A ASP 3.4 4.9 - - - +
264A TRP* 3.6 40.8 - - + +
286A PRO* 6.3 0.2 - - - -
288A ASN* 5.1 14.1 - - - +
293A GLU 4.3 3.4 - - - +
294A HIS* 3.0 40.1 + - + +
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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