Contacts of the strand formed by residues 277 - 281 (chain G) in PDB entry 3KDO
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 ALA 277 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141G PHE* 3.7 27.2 - - + -
146G VAL* 4.6 2.9 - - + -
149G MET* 5.0 1.6 - - - -
250G LYS 2.9 11.2 + - - +
251G HIS* 3.3 32.5 - - + +
252G ALA* 2.8 26.5 + - - +
275G GLY 4.1 0.2 + - - -
276G LEU* 1.3 73.8 - - - +
278G ILE* 1.3 60.1 + - - +
311G ASP* 3.2 15.3 - - + +
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Residues in contact with ILE 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G HIS* 4.9 0.7 - - - -
252G ALA* 3.3 10.3 - - + +
254G VAL* 4.4 17.0 - - + -
267G ILE* 4.8 2.2 - - + +
268G ARG* 3.6 46.0 - - + +
271G ALA* 3.8 22.4 - - + -
272G ALA* 6.2 0.4 - - - -
276G LEU 4.0 2.2 - - - +
277G ALA* 1.3 75.9 - - - +
279G HIS* 1.3 69.2 + - - +
280G GLY* 5.1 0.2 - - - -
309G GLY 4.1 8.1 - - - +
310G ILE* 4.0 22.0 - - + -
311G ASP* 2.6 26.7 + - - +
312G GLN* 3.0 26.8 + - - +
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Residues in contact with HIS 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G TYR* 5.7 0.2 - - - -
189G KCX 3.4 23.0 - - + -
227G PHE* 3.8 35.5 - + + -
251G HIS* 4.8 0.9 - - + -
252G ALA 2.9 12.9 + - - +
253G MET* 3.2 14.4 - - + -
254G VAL 2.8 27.7 + - - +
277G ALA 4.0 0.8 + - - -
278G ILE* 1.3 74.5 - - - +
280G GLY* 1.3 63.9 + - - +
281G HIS 3.9 0.8 + - - -
312G GLN* 3.0 31.0 + - + +
314G HIS* 2.8 36.9 + + - -
365G THR* 3.6 24.5 - - + -
387G VAL* 5.2 0.4 - - + -
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Residues in contact with GLY 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G VAL 3.5 6.1 - - - -
256G VAL* 4.1 9.9 - - - -
278G ILE* 5.1 0.2 - - - -
279G HIS* 1.3 71.6 - - - +
281G HIS* 1.3 61.3 + - - -
310G ILE* 3.6 14.8 - - - +
312G GLN 2.6 19.4 + - - +
313G LEU* 3.7 9.0 - - - +
314G HIS* 3.3 30.3 + - - -
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Residues in contact with HIS 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASN* 3.2 26.7 - - - -
189G KCX 3.2 28.7 - - - -
192G GLU* 3.1 30.3 + - + +
253G MET* 4.0 9.4 - - + -
254G VAL 2.8 9.6 + - - +
255G ASP* 3.3 19.4 - - - +
256G VAL* 3.0 26.2 + - - +
257G VAL 4.1 0.2 + - - -
279G HIS* 3.9 2.5 + - + -
280G GLY* 1.3 71.5 - - - -
282G ARG* 1.3 59.9 + - - +
283G ALA* 3.2 26.5 + - + +
314G HIS* 3.9 16.4 - + + +
600G CAP 2.7 29.8 + - - -
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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
------------------------------------------------------------
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