Contacts of the strand formed by residues 312 - 317 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B TYR* 3.3 40.8 - - + +
286B LEU* 4.1 12.8 - - + -
296B ILE* 3.8 28.9 - - + -
306B PHE* 4.8 3.8 - - + -
307B ASP 3.5 12.6 - - - +
308B ALA* 3.4 24.0 - - + -
311B ARG* 1.3 76.9 - - - +
313B ILE* 1.3 65.5 + - - +
314B TYR* 4.5 7.2 - - + -
327B LEU* 3.3 6.4 - - - +
328B TRP* 3.0 49.7 + - + +
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO* 3.6 28.9 - - + -
21B ARG 4.0 11.2 - - - +
22B THR* 3.9 14.6 - - - -
27B VAL* 3.7 39.3 - - + -
50B LEU* 4.8 1.8 - - + -
306B PHE* 3.1 2.9 - - - +
307B ASP 2.8 47.3 + - - +
311B ARG* 5.0 2.0 - - + -
312B LEU* 1.3 82.0 - - - +
314B TYR* 1.3 62.3 + - - +
325B LEU* 3.9 7.4 - - + -
326B TYR 3.2 10.3 - - - +
327B LEU* 3.6 22.4 - - + -
335B LEU* 4.2 5.2 - - + -
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Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO* 5.0 0.7 - - - -
286B LEU* 3.6 22.2 - - + -
296B ILE* 4.7 1.8 - - + -
297B ALA* 3.9 12.5 - - + +
303B ILE* 3.8 33.2 - - + -
305B GLY 3.2 14.1 - - - +
306B PHE* 3.5 10.8 - - + +
312B LEU* 4.5 4.5 - - + -
313B ILE* 1.3 82.4 - - - +
315B LEU* 1.3 62.4 + - - +
316B LYS* 3.7 4.4 + - + -
325B LEU* 3.8 7.1 - - - +
326B TYR* 2.8 56.3 + + + -
327B LEU 4.8 0.2 + - - -
328B TRP* 3.9 30.3 - - + +
332B GLU* 2.9 39.0 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.5 44.9 - - + +
18B SER* 3.8 11.4 - - - +
19B ASP 4.3 0.2 - - - +
20B PRO* 3.9 26.2 - - + -
29B TYR* 5.6 3.4 - - + -
303B ILE* 3.3 7.8 - - - +
304B MET* 2.9 33.1 + - + -
305B GLY* 2.8 18.3 + - - +
314B TYR* 1.3 74.6 - - - +
316B LYS* 1.3 60.1 + - - +
323B ALA* 4.1 11.4 - - + -
324B GLU* 3.3 17.9 - - - +
325B LEU* 3.7 25.4 - - + +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B HIS* 3.6 40.5 - - + -
302B TRP 3.6 2.2 - - - +
303B ILE* 3.8 13.5 - - + -
314B TYR* 3.7 5.0 + - + -
315B LEU* 1.3 73.9 - - - +
317B GLU* 1.3 61.4 + - - +
318B THR* 4.4 12.2 - - + +
322B PRO 4.4 1.0 - - - +
323B ALA* 3.2 2.5 - - - -
324B GLU* 2.9 27.4 + - - +
326B TYR* 3.3 41.1 + - + +
332B GLU* 3.1 36.8 + - - -
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B HIS* 3.3 5.4 - - - +
302B TRP* 2.9 33.4 + - + +
304B MET* 3.5 33.5 - - + +
315B LEU 4.2 0.4 - - - -
316B LYS* 1.3 74.2 - - - +
318B THR* 1.3 68.0 + - - +
321B ARG 3.4 13.0 - - - +
322B PRO* 4.5 1.3 - - - -
323B ALA* 3.7 25.1 + - + +
394B TYR 4.1 1.0 - - - +
395B TYR* 3.5 13.5 - - - +
396B PHE* 2.6 38.0 + - + +
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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