Contacts of the strand formed by residues 295 - 302 (chain A) in PDB entry 1YHV
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A THR* 2.8 29.9 - - + +
287A ALA 3.3 13.2 - - - +
288A MET* 4.4 7.4 - - + +
293A GLY 3.4 4.4 + - - +
294A GLN* 1.3 84.2 + - - +
296A VAL* 1.3 60.8 + - - +
346A TYR* 3.5 47.4 + - + +
348A ALA* 5.5 1.6 - - - +
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Residues in contact with VAL 296 (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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270A TYR* 3.9 14.6 - - + -
286A THR* 3.3 8.1 - - - +
287A ALA 2.6 47.6 + - - +
289A ASP* 4.5 9.4 - - + +
294A GLN* 3.7 16.4 - - + +
295A GLU* 1.3 79.3 - - - +
297A ALA* 1.3 60.9 + - - +
298A ILE* 3.8 22.2 - - + -
331A LEU* 3.6 26.9 - - + -
343A VAL* 3.9 11.4 - - + -
344A MET 3.4 9.4 - - - +
345A GLU* 4.9 0.2 - - - -
346A TYR* 3.6 7.4 - - - +
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Residues in contact with ALA 297 (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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284A VAL* 4.8 11.4 - - + -
285A TYR 3.3 7.0 - - - +
286A THR* 4.6 1.6 - - - +
296A VAL* 1.3 73.6 - - - +
298A ILE* 1.3 59.5 + - - +
299A ARG 4.2 0.4 + - - -
342A VAL 3.7 1.7 - - - +
343A VAL* 3.7 1.2 - - - -
344A MET* 2.9 43.6 + - + +
345A GLU 4.2 9.6 - - - +
346A TYR* 3.8 17.2 - - + +
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Residues in contact with ILE 298 (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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270A TYR* 3.8 33.0 - - + -
273A PHE* 3.8 27.6 - - + -
283A THR 3.5 2.3 - - - +
284A VAL* 3.3 4.6 - - - +
285A TYR* 2.7 45.5 + - + +
287A ALA* 4.0 5.4 - - + -
296A VAL* 3.8 17.7 - - + -
297A ALA* 1.3 78.2 - - - +
299A ARG* 1.3 67.1 + - - +
300A GLN* 4.4 4.7 - - + -
341A TRP* 3.8 29.6 - - + -
342A VAL 3.4 7.6 - - - +
343A VAL* 4.0 14.6 - - + -
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 3.0 38.9 + - - +
282A GLY* 4.6 0.4 - - - -
283A THR 3.4 7.0 - - - +
284A VAL* 4.3 17.9 - - + +
297A ALA 4.2 0.8 + - - -
298A ILE* 1.3 70.8 - - - +
300A GLN* 1.3 62.7 + - - +
301A MET* 3.6 33.0 - - + +
306A GLN* 6.1 0.4 - - - +
312A ILE* 5.0 4.8 - - - +
315A GLU* 3.4 37.8 + - - -
316A ILE* 6.2 0.2 - - - +
319A MET* 5.5 1.0 - - - +
340A LEU 3.5 1.9 - - - +
341A TRP* 3.3 4.0 - - - -
342A VAL* 3.0 50.3 + - + +
344A MET* 6.0 4.3 - - + +
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Residues in contact with GLN 300 (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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267A LYS* 4.4 7.1 - - - +
273A PHE* 4.1 9.7 - - - -
282A GLY* 3.3 3.8 - - - -
283A THR* 2.8 39.4 + - - +
285A TYR* 3.3 38.2 + - + -
298A ILE* 4.4 3.6 - - + -
299A ARG* 1.3 75.5 - - - +
301A MET* 1.3 61.1 + - - +
339A GLU* 4.7 12.6 - - + +
340A LEU 3.4 4.9 - - - +
341A TRP* 3.2 57.1 - - + +
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Residues in contact with MET 301 (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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281A SER 3.2 22.4 - - - +
282A GLY* 4.6 2.5 - - - -
299A ARG* 3.6 39.7 - - + +
300A GLN* 1.3 77.2 - - - +
302A ASN* 1.3 61.5 + - - +
303A LEU* 3.3 3.2 + - + +
306A GLN* 3.6 24.9 - - + +
312A ILE* 3.2 36.8 - - + -
338A ASP 3.4 0.3 - - - +
339A GLU* 3.4 4.8 - - - +
340A LEU* 2.8 49.5 + - + +
342A VAL* 3.5 28.0 - - + -
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Residues in contact with ASN 302 (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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301A MET* 1.3 72.3 - - - +
303A LEU* 1.3 65.8 + - - +
304A GLN* 2.9 37.8 + - - +
305A GLN* 3.2 43.6 + - + +
306A GLN* 3.4 8.6 + - - +
338A ASP* 3.5 11.4 + - - +
339A GLU* 4.6 9.2 + - - +
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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