Contacts of the strand formed by residues 357 - 363 (chain K) in PDB entry 6T9L
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 357 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158K ASN* 5.1 7.0 - - - +
160K TYR* 3.6 23.6 - - + -
278K VAL* 3.7 9.4 + - + -
279K PHE* 3.6 37.5 - - + +
304K LEU 5.6 0.3 - - - +
355K PRO* 3.8 15.1 - - - +
356K SER* 1.3 91.9 + - - +
358K LEU* 1.3 63.6 + - - +
359K VAL* 3.9 3.4 + - + +
414K ILE* 4.7 9.0 - - + -
464K PHE* 5.2 9.2 - - + -
465K TYR 3.3 19.5 - - - +
466K THR* 4.0 11.2 - - - +
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Residues in contact with LEU 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303K PHE* 4.7 6.1 - - + -
305K ASP* 6.1 0.2 - - - -
306K LEU* 3.8 28.3 - - + -
320K LEU* 6.0 0.2 - - + -
354K LEU* 6.1 0.4 - - + -
355K PRO* 4.5 18.2 - - + -
356K SER 4.1 1.4 - - - -
357K VAL* 1.3 73.4 - - - +
359K VAL* 1.3 68.7 + - - +
360K LEU* 4.0 23.6 - - + -
386K LEU* 5.0 2.5 - - + -
388K MET* 4.3 22.2 - - + -
411K TYR* 3.6 36.6 - - + +
463K LEU 4.0 0.3 - - - +
464K PHE* 3.7 0.9 - - - -
465K TYR* 2.4 51.1 + - + +
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Residues in contact with VAL 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K HIS* 6.5 0.7 - - + -
242K TRP* 4.8 19.5 - - + +
279K PHE* 5.6 5.8 - - + -
304K LEU 3.4 25.8 - - - +
305K ASP* 3.7 14.5 - - + -
306K LEU 3.4 16.2 + - - -
357K VAL* 3.9 4.9 + - + +
358K LEU* 1.3 77.9 - - + +
360K LEU* 1.3 75.4 + - - +
361K GLN* 6.1 0.4 - - + -
462K LEU* 5.1 10.1 - - + -
463K LEU 3.4 14.6 - - - +
464K PHE* 3.6 24.2 - - + -
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Residues in contact with LEU 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K LEU* 3.6 32.1 - - + +
308K LEU* 4.3 23.6 - - + -
316K LEU* 4.5 20.2 - - + -
320K LEU* 5.3 7.0 - - + -
358K LEU* 4.0 18.4 - - + -
359K VAL* 1.3 86.5 - - - +
361K GLN* 1.3 60.7 + - - +
362K LEU* 5.4 2.0 - - + -
386K LEU* 4.5 21.8 - - + -
462K LEU* 3.7 7.3 - - - +
463K LEU* 3.1 44.9 + - + +
465K TYR* 4.7 10.1 - - + -
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Residues in contact with GLN 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K ASP* 5.2 0.2 + - - -
239K HIS* 2.9 46.0 + - + +
305K ASP* 4.5 5.1 - - + +
306K LEU 2.7 16.3 + - - +
307K SER* 3.4 17.9 + - - +
308K LEU* 2.7 35.5 + - - +
359K VAL* 6.1 0.4 - - + -
360K LEU* 1.3 74.5 - - - +
362K LEU* 1.3 67.3 + - - +
363K LYS* 5.6 1.1 - - - -
365K PHE* 5.2 6.3 - - - -
461K TYR* 3.2 24.3 + - + +
462K LEU* 3.9 20.2 - - + -
42O ARG* 4.9 4.0 - - - +
70O VAL* 4.7 13.0 - - - +
71O LEU 5.3 2.4 + - - -
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Residues in contact with LEU 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308K LEU* 3.4 18.8 - - + +
310K ILE* 3.8 27.8 - - + -
316K LEU* 4.5 17.9 - - + -
319K CYS* 5.1 2.7 - - - -
360K LEU* 5.4 2.0 - - + -
361K GLN* 1.3 82.4 - - - +
363K LYS* 1.3 60.9 + - - +
364K ARG* 2.9 31.1 + - + +
380K ILE* 4.5 11.4 - - + -
382K PHE* 6.6 0.2 - - + -
460K ALA* 3.5 22.0 - - + +
461K TYR* 3.4 30.3 + - - +
463K LEU* 4.1 22.0 - - + -
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Residues in contact with LYS 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K SER* 3.2 29.2 + - - +
308K LEU* 3.0 11.5 + - - +
309K ASP* 3.7 25.0 - - + +
310K ILE* 3.7 9.7 + - - +
311K LYS* 5.7 0.2 - - - +
361K GLN* 5.2 2.7 - - - +
362K LEU* 1.3 67.6 - - - +
364K ARG* 1.3 57.3 + - - +
365K PHE* 3.0 46.6 + - + +
376K LEU* 3.5 14.6 - - - +
6O LYS* 5.1 8.9 - - - +
7O THR 3.0 20.8 + - - -
8O LEU* 2.9 30.7 + - - +
10O GLY* 4.1 5.1 - - - +
69O LEU 4.4 5.3 + - - +
70O VAL* 4.0 14.1 - - + -
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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