Contacts of the strand formed by residues 312 - 317 (chain A) in PDB entry 4HXG
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 LEU 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A TYR* 3.7 40.4 - - + +
286A LEU* 3.9 17.3 - - + -
296A ILE* 3.6 36.6 - - + -
306A PHE* 4.7 6.1 - - + -
307A ASP 3.7 11.7 - - - +
308A ALA* 3.7 8.3 - - + -
311A ARG* 1.3 75.2 - - - +
313A ILE* 1.3 70.2 + - - +
314A TYR* 4.3 3.3 - - + -
327A LEU* 3.1 21.6 - - - +
328A TRP* 3.1 31.8 + - + +
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Residues in contact with ILE 313 (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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20A PRO* 3.5 30.3 - - + -
21A ARG 3.9 12.8 - - - +
22A THR* 4.3 8.3 - - - +
27A VAL* 3.4 48.5 - - + -
50A LEU* 5.0 0.7 - - + -
306A PHE* 3.2 4.9 - - - +
307A ASP 3.0 39.1 + - - +
311A ARG* 4.8 2.7 - - + -
312A LEU* 1.3 81.5 - - - +
314A TYR* 1.3 63.4 + - - +
325A LEU* 4.1 7.9 - - + -
326A TYR 3.2 11.9 - - - +
327A LEU* 4.2 11.7 - - + -
335A LEU* 4.6 7.9 - - + -
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Residues in contact with TYR 314 (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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20A PRO* 5.1 0.7 - - - -
286A LEU* 3.5 22.4 - - + -
296A ILE* 4.7 0.7 - - + -
297A ALA* 4.0 18.2 - - + +
303A ILE* 3.8 27.8 - - + -
305A GLY 3.1 14.6 - - - +
306A PHE* 3.6 10.3 - - + +
312A LEU* 4.3 2.9 - - + -
313A ILE* 1.3 82.9 - - - +
315A LEU* 1.3 62.3 + - - +
316A LYS* 4.6 1.6 - - + -
325A LEU* 3.4 7.8 - - - +
326A TYR* 2.7 60.5 + + + +
327A LEU 4.3 2.1 + - - -
328A TRP* 4.2 25.4 - - + +
332A GLU* 2.7 42.2 + - - +
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Residues in contact with LEU 315 (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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17A LEU* 3.7 37.0 - - + +
18A SER* 3.8 10.1 - - - -
19A ASP 4.3 0.2 - - - +
20A PRO* 3.7 31.9 - - + -
29A TYR* 5.4 4.0 - - + -
303A ILE* 3.4 8.5 - - - +
304A MET* 2.9 35.0 + - + -
305A GLY* 2.8 16.7 + - - +
314A TYR* 1.3 73.5 - - - +
316A LYS* 1.3 59.3 + - - +
317A GLU 4.2 0.2 - - - -
323A ALA* 4.1 12.3 - - + -
324A GLU 3.3 7.4 - - - +
325A LEU* 3.3 36.8 - - + -
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Residues in contact with LYS 316 (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 HIS* 3.5 41.2 + - + +
302A TRP 3.6 2.5 - - - +
303A ILE* 4.0 10.3 - - + -
314A TYR* 4.5 3.4 - - + -
315A LEU* 1.3 73.0 - - - +
317A GLU* 1.3 62.5 + - - +
318A THR* 4.1 17.9 - - + +
322A PRO 4.3 1.2 - - - +
323A ALA* 3.2 2.7 - - - -
324A GLU* 2.9 30.5 + - - +
326A TYR* 3.4 38.4 + - + +
332A GLU* 2.9 39.8 + - - -
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Residues in contact with GLU 317 (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 HIS* 3.3 6.2 - - - +
302A TRP* 2.8 34.6 + - + +
304A MET* 3.7 37.6 - - + +
315A LEU 4.2 0.4 - - - -
316A LYS* 1.3 73.0 - - - +
318A THR* 1.3 67.3 + - - +
321A ARG 3.3 17.0 - - - +
322A PRO* 4.6 1.5 - - - +
323A ALA* 3.9 20.0 + - - +
394A TYR 4.4 0.4 - - - -
395A TYR* 3.6 10.0 - - - +
396A PHE* 2.8 35.0 + - + +
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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