Contacts of the strand formed by residues 291 - 301 (chain A) in PDB entry 5U2H
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.6 36.6 - + + -
248A GLN 3.9 1.8 + - - +
249A GLY* 3.5 7.3 - - - -
250A GLY 3.6 8.3 - - - +
251A ILE* 3.3 33.9 - - + -
290A GLY* 1.3 73.2 - - - -
292A ASN* 1.3 64.5 + - - +
293A PHE* 3.9 21.2 - + - -
313A PHE* 3.1 7.3 - - - +
314A GLY 2.9 40.7 + - - +
316A ARG* 3.9 14.6 - - + +
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Residues in contact with ASN 292 (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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288A TYR* 3.7 36.7 - - - +
289A PRO 4.4 10.3 - - - +
290A GLY 4.5 1.7 - - - +
291A TYR* 1.3 79.2 - - - +
293A PHE* 1.3 66.1 + - - +
311A LYS* 4.2 15.0 - - + +
312A VAL 2.6 19.3 - - - +
313A PHE* 3.3 33.8 - - + -
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Residues in contact with PHE 293 (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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95A PHE* 4.8 16.8 - + - -
103A PHE* 4.1 31.0 - + - -
291A TYR* 3.9 31.6 - + - -
292A ASN* 1.3 78.5 - - - +
294A ARG* 1.3 67.3 + - - +
295A TYR* 4.1 23.3 - + + -
310A ILE 3.5 1.0 - - - +
311A LYS* 3.7 3.8 - - - +
312A VAL* 2.9 48.8 + - + +
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Residues in contact with ARG 294 (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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143A GLN 4.9 8.5 + - - -
145A LYS* 3.8 27.9 - - - +
171A GLU* 2.8 32.5 + - - +
288A TYR* 5.3 5.1 + - - -
293A PHE* 1.3 75.9 - - - +
295A TYR* 1.3 59.2 + - - +
296A ALA 4.5 0.2 + - - -
309A LEU* 4.1 26.2 - - + +
310A ILE 3.6 6.3 - - - +
311A LYS* 3.4 28.0 - - - +
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Residues in contact with TYR 295 (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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95A PHE* 4.1 32.3 - + - -
293A PHE* 3.7 20.4 + + + -
294A ARG* 1.3 74.1 - - - +
296A ALA* 1.3 75.3 + - - +
297A LYS* 5.3 5.8 - - + -
308A THR 3.9 0.5 - - - +
309A LEU* 4.8 0.9 - - - -
310A ILE* 2.9 47.2 + - + +
312A VAL* 4.3 8.3 - - + -
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Residues in contact with ALA 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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294A ARG 4.3 0.4 - - - -
295A TYR* 1.3 90.8 - - - +
297A LYS* 1.3 61.0 + - - +
298A TYR* 3.8 35.4 - - + +
307A ARG* 5.1 0.9 - - + -
308A THR 3.0 13.5 - - - +
309A LEU* 3.6 22.7 - - + -
403A 7S1 6.0 1.2 - - - +
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Residues in contact with LYS 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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295A TYR* 5.3 6.5 - - + -
296A ALA* 1.3 75.8 - - - +
298A TYR* 1.3 64.2 + - - +
299A TYR* 3.9 6.7 + - + -
307A ARG* 3.7 0.5 - - - -
308A THR* 2.9 39.2 + - + +
310A ILE* 6.3 2.9 - - + -
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Residues in contact with TYR 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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167A TRP* 4.8 8.3 - + - -
296A ALA* 3.8 28.2 - - + +
297A LYS* 1.3 73.7 - - - +
299A TYR* 1.3 62.0 + - - +
305A GLU* 4.5 14.1 - - - +
306A LYS 3.4 8.7 - - - +
307A ARG* 3.3 27.4 - - + -
403A 7S1 3.4 81.5 + + + +
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Residues in contact with TYR 299 (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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112A GLU* 5.0 3.0 - - + +
113A GLY* 3.7 24.8 + - - -
297A LYS* 4.0 9.9 - - + -
298A TYR* 1.3 73.9 - - - +
300A LYS* 1.3 69.6 + - - +
301A GLU* 4.1 15.3 - - + -
305A GLU* 5.2 2.9 - - - -
306A LYS* 2.8 56.7 + - + +
307A ARG 4.7 0.4 - - - -
308A THR* 3.1 26.8 + - - -
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Residues in contact with LYS 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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299A TYR* 1.3 76.7 - - - +
301A GLU* 1.3 60.2 + - - +
303A ASN* 5.2 3.8 - - - -
304A VAL 3.3 16.6 - - - +
305A GLU* 4.6 11.4 - - - +
306A LYS 4.5 0.4 - - - +
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Residues in contact with GLU 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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299A TYR* 4.0 22.1 + - + -
300A LYS* 1.3 74.6 - - - +
302A ASN* 1.3 73.7 + - + +
303A ASN 3.2 1.6 - - - -
304A VAL* 2.9 26.2 + - - +
306A LYS* 5.3 2.9 - - + -
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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