Contacts of the helix formed by residues 361 - 370 (chain U) in PDB entry 6FF7
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 THR 361 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357U ALA 4.9 6.2 + - - -
359U VAL 3.4 1.4 - - - -
360U ASP* 1.3 80.4 - - - +
362U ARG* 1.3 66.6 + - - +
363U GLU* 4.1 11.4 - - - -
364U SER* 3.1 11.3 + - - -
365U LEU* 2.9 23.5 + - - +
412U GLU* 4.6 0.7 - - - -
413U ARG* 4.6 7.9 - - - +
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Residues in contact with ARG 362 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360U ASP 3.9 0.6 + - - -
361U THR* 1.3 72.9 - - - +
363U GLU* 1.3 57.4 + - - +
365U LEU* 3.3 5.3 + - - +
366U VAL* 2.9 31.2 + - - +
408U VAL* 5.5 7.1 - - + +
412U GLU* 4.0 21.8 - - + +
413U ARG* 5.0 0.4 - - - +
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Residues in contact with GLU 363 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361U THR* 3.1 7.6 - - - -
362U ARG* 1.3 79.7 - - - +
364U SER* 1.3 56.4 + - - +
366U VAL* 3.5 5.7 + - - +
367U LYS* 3.0 26.9 + - - +
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Residues in contact with SER 364 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358U GLU 3.6 24.0 - - - -
359U VAL* 3.7 16.6 - - - -
361U THR* 3.1 15.9 + - - -
363U GLU* 1.3 79.9 - - - +
365U LEU* 1.3 58.0 + - - +
367U LYS* 3.2 9.0 + - - +
368U PHE* 2.9 29.9 + - - +
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Residues in contact with LEU 365 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359U VAL 3.9 9.6 + - - +
360U ASP 5.6 0.9 - - - -
361U THR 2.9 16.8 + - - +
362U ARG* 3.7 7.2 - - - +
364U SER* 1.3 73.7 - - - +
366U VAL* 1.3 61.4 + - - +
368U PHE* 3.3 5.1 + - - +
369U PHE* 2.9 35.7 + - + +
408U VAL* 4.6 24.2 - - + +
411U HIS* 5.9 4.9 - - + -
412U GLU* 5.8 2.9 - - + +
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Residues in contact with VAL 366 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362U ARG 2.9 17.4 + - - +
363U GLU* 3.8 5.4 - - - +
365U LEU* 1.3 76.9 - - - +
367U LYS* 1.3 58.9 + - - +
369U PHE* 5.4 0.2 - - - -
370U GLY* 2.8 34.4 + - - +
371U PRO 4.4 0.2 - - - -
408U VAL* 5.5 4.6 - - + +
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Residues in contact with LYS 367 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363U GLU 3.0 15.6 + - - +
364U SER* 3.3 12.6 - - - +
366U VAL* 1.3 78.6 - - - +
368U PHE* 1.3 59.5 + - - +
370U GLY 4.6 0.5 + - - -
371U PRO* 4.7 9.7 - - - +
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Residues in contact with PHE 368 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347U GLU 5.7 1.0 - - - +
348U LEU* 5.9 3.9 - - + +
351U PHE* 4.5 22.2 - - + -
359U VAL* 6.3 2.5 - - + -
364U SER 2.9 15.5 + - - +
365U LEU* 4.0 4.9 - - - +
366U VAL 3.2 0.2 - - - -
367U LYS* 1.3 79.6 - - - +
369U PHE* 1.3 60.0 + - + +
370U GLY 3.7 0.2 - - - -
371U PRO* 4.9 4.7 - - - +
372U LEU* 5.1 5.0 + - - +
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Residues in contact with PHE 369 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365U LEU* 2.9 14.8 + - + +
366U VAL* 5.4 0.2 - - - -
368U PHE* 1.3 75.8 - - + +
370U GLY* 1.3 67.3 + - - +
371U PRO 3.4 2.5 - - - -
372U LEU* 3.2 24.1 + - + +
377U LEU* 5.6 6.5 - - + +
404U LEU* 5.6 10.6 - - + +
407U LEU* 5.5 11.4 - - + -
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Residues in contact with GLY 370 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366U VAL* 2.8 24.5 + - - +
369U PHE* 1.3 80.1 - - - +
371U PRO* 1.3 60.3 - - - +
372U LEU 3.3 6.2 + - - +
404U LEU* 5.7 8.3 - - - -
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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