Contacts of the strand formed by residues 305 - 311 (chain A) in PDB entry 3V4K
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 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ILE* 5.1 5.6 - - + -
271A LEU* 4.0 17.3 - - + -
277A TYR* 3.7 3.8 - - + -
279A VAL* 3.9 24.0 - - + -
298A PHE* 4.6 13.5 - - + -
299A ILE* 4.7 17.7 - - + +
302A ASN* 3.0 22.7 + - + +
303A LYS* 3.1 7.6 + - - +
304A HIS* 1.3 104.1 - - + +
306A SER* 1.3 71.9 + - - +
307A LEU* 4.0 10.3 + - + +
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Residues in contact with SER 306 (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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232A TRP* 4.7 10.7 - - - -
277A TYR 2.8 15.0 + - - -
278A ARG* 3.3 14.9 - - - +
279A VAL 2.8 26.2 + - - +
303A LYS 5.6 0.7 + - - -
304A HIS 4.2 0.2 - - - -
305A VAL* 1.3 74.9 + - - +
307A LEU* 1.3 59.9 + - - +
308A CYS* 5.9 1.6 - - - -
334A LYS* 6.3 2.9 - - - -
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Residues in contact with LEU 307 (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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262A PHE* 4.1 13.9 - - + -
263A LEU* 6.1 1.8 - - + -
266A ILE* 6.2 0.2 - - + -
279A VAL* 3.5 18.6 - - + +
281A CYS* 4.1 23.6 - - - -
295A MET* 4.1 25.6 - - + -
299A ILE* 4.0 32.8 - - + +
305A VAL* 4.0 5.4 + - + -
306A SER* 1.3 72.1 - - - +
308A CYS* 1.3 66.7 + - - +
309A ILE* 4.1 16.8 - - + -
328A LEU* 4.7 4.5 - - + -
332A GLY 4.3 3.8 + - - +
333A ALA* 3.4 17.9 - - + +
334A LYS* 2.9 24.3 + - - +
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Residues in contact with CYS 308 (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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278A ARG* 4.0 31.4 - - - -
279A VAL 2.9 6.7 + - - +
280A THR* 3.4 19.6 - - + +
281A CYS* 2.8 28.2 + - - +
306A SER* 4.9 1.8 - - - -
307A LEU* 1.3 79.6 - - - +
309A ILE* 1.3 63.6 + - - +
310A LYS* 4.0 13.9 - - - -
334A LYS* 3.3 31.0 - - - +
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Residues in contact with ILE 309 (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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281A CYS* 3.5 7.4 - - + -
283A THR* 4.0 27.8 - - + +
287A PRO* 4.8 14.1 - - + -
295A MET* 3.8 22.0 - - + -
307A LEU* 4.1 19.5 - - + -
308A CYS* 1.3 76.7 - - - +
310A LYS* 1.3 64.5 + - - +
311A THR* 4.6 6.5 - - + -
328A LEU* 3.4 34.5 - - + -
333A ALA* 4.6 2.2 - - + -
334A LYS 2.8 11.5 + - - +
335A ILE* 3.3 18.9 - - + +
336A SER* 2.9 27.0 + - - +
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Residues in contact with LYS 310 (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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280A THR* 4.1 18.6 + - + +
281A CYS 2.9 12.8 + - - +
282A PHE* 3.2 34.9 - - + -
283A THR* 2.9 23.9 + - - -
308A CYS* 4.6 12.3 - - + -
309A ILE* 1.3 76.8 - - - +
311A THR* 1.3 60.7 + - - +
334A LYS 5.7 0.4 - - - +
336A SER* 3.3 22.0 - - - +
337A ILE 5.3 0.2 - - - -
338A MET* 3.7 14.2 - - + +
342A GLU* 4.1 19.9 + - + +
369B GLN* 5.9 2.6 - - - +
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Residues in contact with THR 311 (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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283A THR* 3.1 22.1 + - - -
285A TRP 3.2 2.4 - - - -
286A SER* 3.1 24.2 + - - -
309A ILE* 4.6 5.2 - - - -
310A LYS* 1.3 72.4 - - - +
312A ALA* 1.3 63.3 + - - +
313A ARG 2.9 26.6 + - - +
314A ILE* 4.9 1.8 - - + -
335A ILE* 5.0 9.2 - - + -
336A SER 2.9 18.3 + - - +
337A ILE* 3.4 21.8 - - + +
338A MET* 2.9 22.8 + - - +
375A LEU* 6.2 0.2 - - + -
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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