Contacts of the strand formed by residues 312 - 319 (chain E) in PDB entry 6XAV
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 SER 312 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170E ARG* 3.3 24.7 - - - +
171E GLY* 3.5 21.6 + - - -
254E VAL* 3.5 10.6 - - - +
258E LYS 3.1 6.6 + - - +
259E ASP* 3.1 19.9 + - - +
260E VAL 2.9 26.9 + - - +
261E ILE* 6.1 0.5 - - - +
305E ARG 4.0 4.7 - - - -
306E ASN* 3.9 7.0 - - - -
307E VAL 4.5 1.1 - - - +
311E GLY* 1.3 76.5 - - - -
313E LEU* 1.3 60.9 + - - +
314E THR* 4.6 1.6 + - - -
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Residues in contact with LEU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E PHE* 4.4 13.5 - - + -
171E GLY* 3.3 7.4 - - - -
247E ILE* 4.0 11.9 - - + -
250E ALA* 3.8 27.6 - - + -
251E LYS* 4.7 7.0 - - + -
254E VAL* 3.9 11.6 - - + +
260E VAL* 3.4 14.8 - - + +
262E ILE* 4.3 14.1 - - + -
303E ALA* 3.3 38.8 - - + +
304E ALA* 3.4 11.0 - - - +
305E ARG 3.2 32.0 + - - +
312E SER* 1.3 73.1 - - - +
314E THR* 1.3 60.5 + - - +
315E ILE* 4.4 6.1 - - + -
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Residues in contact with THR 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E LEU* 4.6 2.3 - - + +
168E ILE* 4.6 6.1 - - + -
169E GLY 3.6 8.9 + - - +
170E ARG* 3.8 2.4 - - - -
171E GLY 2.8 26.5 + - - -
172E GLN 3.3 20.0 + - - +
195E ILE* 6.0 1.1 - - + -
260E VAL 2.9 7.8 + - - +
261E ILE* 3.2 30.0 - - + +
262E ILE* 2.7 32.1 + - - +
312E SER* 4.6 2.3 + - - -
313E LEU* 1.3 71.0 - - - +
315E ILE* 1.3 59.2 + - - +
316E ILE* 3.9 21.1 - - + -
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Residues in contact with ILE 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E GLN 3.4 4.2 + - - -
173E ARG* 3.7 7.4 - - + +
174E GLY 3.6 22.2 + - - +
247E ILE* 4.5 10.5 - - + -
262E ILE* 3.4 20.6 - - + +
264E LEU* 5.6 3.1 - - + -
300E PHE* 3.8 52.9 - - + +
301E PHE* 4.6 12.5 - - + +
304E ALA* 3.8 27.8 - - + +
313E LEU* 4.4 8.3 - - + -
314E THR* 1.3 79.1 - - - +
316E ILE* 1.3 63.3 + - - +
317E ALA* 3.9 14.1 + - + +
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Residues in contact with ILE 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ILE* 3.9 32.3 - - + -
172E GLN* 4.0 11.4 - - + +
174E GLY* 3.8 23.1 - - - +
176E ILE* 3.7 31.0 - - + -
188E LEU* 4.7 2.5 - - + +
191E ILE* 4.5 15.0 - - + -
195E ILE* 6.2 1.8 - - + -
261E ILE* 5.4 0.7 - - + -
262E ILE 3.2 7.6 + - - -
263E LEU* 3.8 36.7 - - + +
264E LEU 3.9 2.3 + - - -
265E ASP* 4.2 5.5 - - - +
314E THR* 3.9 16.1 - - + -
315E ILE* 1.3 79.0 - - - +
317E ALA* 1.3 59.7 + - - +
318E THR* 5.2 0.3 - - - +
341E MET* 5.2 0.7 - - - -
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Residues in contact with ALA 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E GLY 3.4 6.0 + - - +
175E LEU* 3.3 24.2 - - + -
176E ILE* 2.8 30.7 + - - +
264E LEU* 3.2 20.2 - - + +
267E ILE* 4.1 17.9 - - + -
300E PHE* 6.4 1.1 - - + -
301E PHE* 5.2 2.9 - - + -
315E ILE* 3.9 13.3 - - + -
316E ILE* 1.3 75.1 - - - +
318E THR* 1.3 57.0 + - - +
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Residues in contact with THR 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E LEU* 5.2 0.2 - - - -
176E ILE* 3.3 37.2 - - + -
184E LYS* 3.9 34.1 - - + +
187E LEU* 5.9 1.1 - - + -
188E LEU* 5.3 3.1 - - + -
264E LEU 4.0 1.2 + - - -
265E ASP* 3.2 43.5 + - - +
267E ILE* 3.3 19.8 + - - +
316E ILE 5.2 0.7 - - - +
317E ALA* 1.3 76.7 - - - +
319E ALA* 1.3 60.8 + - - +
320E LEU* 4.1 8.5 - - - +
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Residues in contact with ALA 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E LEU* 5.0 12.6 - - + -
176E ILE 2.7 11.6 + - - +
177E VAL* 4.2 19.1 - - + -
178E ALA* 2.8 28.4 + - - +
184E LYS* 4.4 1.2 - - - +
267E ILE* 4.3 7.4 - - + -
268E THR* 4.1 7.9 - - - +
317E ALA 4.2 0.6 + - - -
318E THR* 1.3 73.3 - - - +
320E LEU* 1.3 65.7 + - - +
321E ILE* 5.2 0.2 - - - -
332E TYR* 4.6 16.6 - - + -
335E PHE* 6.4 2.7 - - + -
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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