Contacts of the strand formed by residues 281 - 288 (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 GLY 281 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279K PHE 3.5 3.0 + - - -
280K GLU* 1.3 77.8 - - - +
282K SER* 1.3 64.7 + - - -
302K PRO* 3.3 20.6 - - - +
303K PHE* 2.9 31.3 + - - -
353K LYS* 3.9 11.0 - - - -
355K PRO* 4.3 7.1 - - - +
59N ASN* 4.8 4.0 - - - -
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Residues in contact with SER 282 (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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281K GLY* 1.3 75.5 - - - -
283K LEU* 1.3 60.1 + - - +
300K ILE* 3.8 23.1 - - - -
301K ASP 3.5 6.7 - - - -
302K PRO* 3.8 5.6 - - - -
303K PHE* 3.2 11.9 - - - -
351K ILE* 4.2 2.1 - - - +
352K HIS* 3.2 23.2 + - - +
353K LYS* 3.2 39.1 + - - +
59N ASN* 5.0 0.5 + - - -
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Residues in contact with LEU 283 (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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282K SER* 1.3 74.9 - - - +
284K GLU* 1.3 63.1 + - - +
299K THR 4.6 0.2 - - - -
300K ILE* 3.4 14.7 - - - +
301K ASP* 2.6 41.0 + - + +
302K PRO 5.4 0.4 - - - +
303K PHE* 3.6 33.9 - - + -
306K LEU* 4.3 12.6 - - + -
323K PHE* 4.6 16.2 - - + -
349K LEU* 5.7 12.6 - - + -
350K GLY 3.5 4.9 - - - +
351K ILE* 3.7 28.5 - - + -
352K HIS* 4.1 1.6 - - - +
66O THR* 6.0 4.5 - - + -
68O HIS* 4.7 22.0 - - + +
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Residues in contact with GLU 284 (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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283K LEU* 1.3 78.6 - - - +
285K SER* 1.3 66.7 + - - +
286K SER* 4.4 10.0 + - - +
298K THR* 4.1 20.5 - - + +
299K THR 3.8 4.5 - - - +
300K ILE* 3.9 14.8 - - + -
348K GLN 3.9 0.5 - - - +
349K LEU* 3.4 4.7 - - - +
350K GLY* 2.5 50.3 + - - +
352K HIS* 3.6 21.2 + - + +
393K SER* 3.3 28.3 + - - +
394K THR* 5.2 4.0 + - - -
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Residues in contact with SER 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284K GLU* 1.3 73.9 - - - +
286K SER* 1.3 66.2 + - - +
287K ILE* 5.2 11.0 - - - +
297K LYS 4.2 2.8 - - - +
298K THR* 4.0 7.4 - - - -
299K THR* 2.4 52.0 + - - +
301K ASP* 4.6 3.4 + - - -
347K LYS* 5.3 3.4 - - - -
348K GLN 3.6 4.0 - - - -
349K LEU* 3.8 19.1 - - - -
4O PHE* 6.3 1.3 - - - -
64O GLU 4.8 4.9 + - - -
66O THR* 4.7 8.9 + - - -
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Residues in contact with SER 286 (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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284K GLU* 4.4 14.7 + - - +
285K SER* 1.3 77.6 + - - +
287K ILE* 1.3 65.8 + - - +
288K VAL* 3.7 14.8 - - - +
295K ASN 5.9 0.4 - - - -
296K SER* 4.7 10.8 - - - -
297K LYS 5.4 0.7 - - - -
298K THR* 4.8 7.1 - - - +
346K ILE 3.4 2.9 - - - +
347K LYS* 3.4 2.4 - - - -
348K GLN* 2.9 43.5 + - - +
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Residues in contact with ILE 287 (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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285K SER* 5.2 6.1 - - - -
286K SER* 1.3 81.7 - - - +
288K VAL* 1.3 60.7 + - - +
289K CYS 3.3 2.1 + - - -
295K ASN* 3.2 19.1 + - - +
296K SER* 3.2 22.3 + - - +
297K LYS* 5.5 3.6 - - - +
329K LEU* 3.8 18.4 - - + -
332K PHE* 4.9 10.5 - - + -
334K TYR* 5.0 5.6 + - + -
345K ALA* 3.6 21.8 - - + +
346K ILE 3.3 4.5 - - - +
347K LYS* 4.0 19.1 - - + -
4O PHE* 3.8 31.4 - - + -
64O GLU* 5.0 12.8 - - - +
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Residues in contact with VAL 288 (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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286K SER* 4.4 17.9 - - - +
287K ILE* 1.3 69.6 - - - +
289K CYS* 1.3 69.5 + - - +
290K PRO* 5.5 0.7 - - + -
293K GLN* 5.0 16.6 - - + -
295K ASN* 3.7 18.6 - - + +
326K LYS* 5.8 8.3 - - + +
345K ALA* 3.3 0.8 - - - -
346K ILE* 2.4 61.8 + - + +
348K GLN* 4.9 12.8 - - + +
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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