Contacts of the strand formed by residues 315 - 321 (chain S) in PDB entry 6O81
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 PHE 315 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200L GLY 4.4 3.1 + - - +
201L TYR* 3.3 51.4 - + + +
293S GLU* 5.5 7.4 - - + -
294S ILE 3.4 17.5 - - - +
295S GLU* 3.7 24.0 - - + -
313S PRO* 3.6 30.9 + - + -
314S LYS* 1.3 72.3 - - - +
316S SER* 1.3 59.8 + - - +
362S GLY* 6.0 2.5 - - - -
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Residues in contact with SER 316 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L TYR* 4.8 3.6 - - - -
293S GLU* 4.5 2.5 - - - -
294S ILE* 2.9 34.4 + - - +
314S LYS* 3.9 4.1 + - - -
315S PHE* 1.3 75.6 - - - +
317S LYS* 1.3 62.9 + - - +
341S THR* 4.0 13.7 - - - -
342S LYS* 3.8 28.5 - - - -
343S ILE* 4.2 10.1 - - - -
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Residues in contact with LYS 317 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201L TYR* 5.5 10.1 - - + -
291S GLY* 4.5 13.7 - - - +
292S GLN 3.9 4.9 - - - -
293S GLU* 4.1 10.0 - - + +
316S SER* 1.3 71.8 - - - +
318S ILE* 1.3 60.8 + - - +
319S VAL* 3.1 5.8 + - - +
341S THR* 3.4 0.6 - - - -
342S LYS* 3.0 35.0 + - + +
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Residues in contact with ILE 318 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289S LYS 4.3 14.4 - - - +
290S VAL* 3.7 2.6 - - - -
291S GLY* 2.7 32.4 + - - -
292S GLN* 3.0 20.4 + - + +
294S ILE* 5.2 7.0 - - + -
316S SER 3.5 2.4 + - - +
317S LYS* 1.3 67.6 - - - +
319S VAL* 1.3 63.0 + - - +
320S SER 3.5 7.4 - - - +
339S VAL* 5.4 8.5 - - + -
340S GLY 4.5 0.4 - - - -
341S THR* 4.0 12.1 - - - +
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Residues in contact with VAL 319 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S VAL* 4.1 9.6 - - - +
291S GLY 5.0 0.2 + - - -
317S LYS 3.1 9.0 + - - +
318S ILE* 1.3 74.8 - - - +
320S SER* 1.3 64.3 + - - +
340S GLY 3.1 14.4 + - - +
341S THR 4.4 6.7 - - - -
342S LYS* 4.7 4.7 - - + +
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Residues in contact with SER 320 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S VAL* 4.7 7.2 - - - -
318S ILE* 3.5 6.1 - - - +
319S VAL* 1.3 80.1 + - - +
321S LEU* 1.3 62.6 + - - +
322S PHE* 3.8 7.6 - - - -
339S VAL* 3.5 5.0 - - - +
340S GLY* 2.9 34.6 + - - +
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Residues in contact with LEU 321 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288S LEU* 5.4 0.7 - - + +
289S LYS 6.1 0.4 - - - -
290S VAL* 5.0 5.2 - - + +
320S SER* 1.3 73.3 - - - +
322S PHE* 1.3 58.6 + - - +
323S ALA 3.8 0.2 - - - -
327S ASP* 3.3 26.0 - - + +
328S LEU 3.8 17.3 + - - +
329S GLN* 4.2 13.0 - - - +
331S ALA* 4.4 18.8 - - + -
338S GLY 3.2 9.9 - - - +
339S VAL* 4.4 4.5 - - + +
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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
------------------------------------------------------------
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