Contacts of the strand formed by residues 310 - 315 (chain P) in PDB entry 5IYB
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 VAL 310 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261P SER* 3.2 7.6 - - - -
262P CYS* 2.9 45.4 + - - +
264P VAL* 5.1 4.9 - - + -
302P LEU* 4.2 16.4 - - + -
303P LEU 3.4 8.3 - - - +
304P ILE* 4.3 21.1 - - + -
308P GLY 3.5 11.0 - - - +
309P LYS* 1.3 80.4 - - - +
311P VAL* 1.3 69.5 + - - +
312P LEU* 3.9 19.3 - - + -
325P PHE* 5.4 6.5 - - + -
328P ILE* 5.6 0.4 - - + -
332P LEU* 4.3 19.5 - - + -
82Y T 5.8 0.2 - - - +
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Residues in contact with VAL 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259P VAL* 4.2 12.6 - - + -
260P GLY 3.5 11.0 - - - +
261P SER* 4.1 10.5 - - - -
302P LEU* 3.3 5.0 - - - +
303P LEU* 2.8 52.1 + - + +
305P PHE* 4.5 6.1 - - + -
310P VAL* 1.3 77.7 - - - +
312P LEU* 1.3 70.1 + - - +
313P THR* 5.9 0.2 - - - -
12X T 5.6 0.2 - - - +
81Y A 3.4 39.0 - - + +
82Y T 4.1 26.5 - - - +
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Residues in contact with LEU 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P PRO* 6.4 0.7 - - + -
258P MET 4.0 0.2 - - - +
259P VAL* 3.3 9.8 - - - +
260P GLY 2.8 45.1 + - - +
261P SER* 4.4 3.1 - - - -
262P CYS* 5.0 8.7 - - - -
300P ILE* 4.2 11.9 - - + -
301P VAL 3.5 4.7 - - - -
302P LEU* 3.6 30.7 - - + -
310P VAL* 3.9 16.4 - - + +
311P VAL* 1.3 83.3 - - - +
313P THR* 1.3 61.7 + - - +
321P ILE* 3.7 39.5 - - + +
324P ALA* 4.2 13.7 - - + -
325P PHE* 4.5 10.1 - - + +
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Residues in contact with THR 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257P ASN* 3.1 13.2 + - - -
258P MET 3.7 7.6 - - - -
259P VAL* 4.1 12.4 - - - +
300P ILE* 3.4 7.5 - - - +
301P VAL* 2.8 48.6 + - + +
303P LEU* 4.6 3.8 - - + -
311P VAL* 5.9 0.2 - - - -
312P LEU* 1.3 77.9 - - - +
314P GLY* 1.3 65.2 + - - +
315P ALA* 3.3 4.5 - - - -
321P ILE* 5.3 0.2 - - - -
12X T 4.4 19.3 - - - +
13X A 2.7 38.6 + - + +
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Residues in contact with GLY 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257P ASN* 3.0 13.4 + - - -
298P PRO 4.9 0.3 - - - +
299P ARG 3.9 13.0 - - - +
300P ILE* 3.7 6.4 - - - +
301P VAL* 4.9 0.9 - - - -
313P THR* 1.3 82.6 + - - +
315P ALA* 1.3 61.4 + - - +
316P LYS* 3.5 18.8 + - - +
320P GLU* 4.9 0.2 - - - +
13X A 4.1 4.0 - - - -
14X A 3.8 20.7 + - - -
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Residues in contact with ALA 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257P ASN* 3.2 10.4 + - - +
258P MET* 2.8 36.3 + - + +
300P ILE* 3.5 17.0 - - + +
313P THR 3.3 1.2 - - - -
314P GLY* 1.3 79.8 - - - +
316P LYS* 1.3 61.4 + - - +
317P VAL 4.0 6.5 - - - +
320P GLU* 3.4 10.1 - - + +
321P ILE* 3.7 30.1 - - + -
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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