Contacts of the helix formed by residues 355 - 360 (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 ASN 355 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273M GLU* 6.0 1.6 - - + -
276M ARG* 5.8 6.3 - - + -
305M SER* 5.2 9.0 - - - -
306M MET* 3.8 10.3 - - - +
309M ALA* 3.0 8.3 - - - +
310M LYS 4.5 0.8 - - - +
311M MET* 4.9 5.4 - - - +
312M GLU* 4.4 16.1 - - + +
313M THR* 4.8 12.1 - - - +
353U LEU 4.0 0.2 + - - -
354U SER* 1.3 77.8 - - - +
356U VAL* 1.3 66.4 + - - +
357U ALA* 3.3 7.0 - - + +
358U GLU* 3.1 23.0 + - + +
359U VAL* 3.6 5.9 + - - +
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Residues in contact with VAL 356 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273M GLU* 3.4 30.9 - - + +
305M SER 5.5 0.6 + - - -
306M MET* 4.7 3.0 - - - +
331U TYR* 5.7 6.7 - - + -
334U ILE* 4.9 17.5 - - + -
354U SER 3.7 1.6 + - - -
355U ASN* 1.3 72.8 - - - +
357U ALA* 1.3 63.2 + - - +
359U VAL* 3.0 5.3 + - - +
360U ASP* 3.0 31.5 + - + +
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Residues in contact with ALA 357 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273M GLU* 5.1 2.5 - - - +
276M ARG* 4.9 23.0 - - + +
277M ASP* 5.3 6.1 - - + +
280M GLU* 5.8 4.7 - - + -
355U ASN* 3.3 4.3 - - + +
356U VAL* 1.3 78.2 - - - +
358U GLU* 1.3 60.6 + - - +
359U VAL 3.5 0.3 + - - -
360U ASP* 4.2 7.4 + - - +
361U THR* 4.9 5.9 + - - -
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Residues in contact with GLU 358 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312M GLU* 4.8 12.6 - - + -
354U SER* 4.5 12.6 - - - -
355U ASN* 3.1 19.1 + - + +
356U VAL 3.1 1.4 - - - -
357U ALA* 1.3 77.6 - - - +
359U VAL* 1.3 57.2 + - - +
364U SER* 3.6 14.4 - - - -
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Residues in contact with VAL 359 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351U PHE* 4.7 20.6 - - + +
354U SER* 4.9 5.4 - - - +
355U ASN 3.6 7.4 + - - +
356U VAL* 3.0 6.7 + - - +
358U GLU* 1.3 80.7 - - - +
360U ASP* 1.3 60.7 + - - +
361U THR 3.4 6.6 + - - +
364U SER* 3.7 15.3 - - - +
365U LEU* 3.9 11.3 + - - +
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Residues in contact with ASP 360 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334U ILE* 5.3 10.8 - - + -
356U VAL* 3.0 20.9 + - + +
357U ALA* 4.2 4.9 + - - +
358U GLU 3.8 0.2 - - - -
359U VAL* 1.3 76.8 - - - +
361U THR* 1.3 61.0 + - - +
365U LEU* 5.6 0.9 - - - -
411U HIS* 4.3 12.3 - - - +
412U GLU* 3.3 8.0 - - - -
413U ARG* 2.9 32.8 + - + +
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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