Contacts of the helix formed by residues 337 - 345 (chain A) in PDB entry 1GNG
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 HIS 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A GLU* 3.6 15.5 - - + -
315A ALA* 4.4 8.4 + - + +
316A LEU* 3.5 45.7 + - + +
319A ARG* 5.3 1.0 - - + +
329A LEU* 4.2 13.2 - - + -
333A GLU 3.2 6.1 + - - +
334A ALA* 3.0 23.2 + - - +
335A CYS 3.2 0.4 - - - -
336A ALA* 1.3 78.7 - - - +
338A SER* 1.3 65.4 + - - +
339A PHE* 3.0 32.0 + - - +
340A PHE* 2.9 25.2 + - + +
344A ARG* 3.1 11.0 + - - -
312B GLU* 5.3 0.4 + - - -
337B HIS* 6.3 0.4 - - - -
338B SER* 4.2 25.8 + - - -
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 3.1 33.6 - - - +
336A ALA 3.7 1.8 + - - -
337A HIS* 1.3 83.2 + - - +
339A PHE* 1.3 61.2 + - - +
340A PHE 3.1 0.2 - - - -
341A ASP* 3.2 37.8 + - - +
319B ARG* 3.8 0.6 + - - -
329B LEU* 6.5 0.9 - - - -
337B HIS* 3.8 26.3 + - - -
338B SER* 4.8 5.9 + - - -
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Residues in contact with PHE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 4.3 8.7 - - + -
158A VAL* 3.8 25.1 - - + -
159A LYS* 3.4 60.6 + - + +
162A MET* 5.0 0.9 - - + -
247A LEU* 4.9 4.7 - - + -
251A LEU* 5.6 0.2 - - + -
310A PRO* 4.8 4.5 - - + -
312A GLU* 3.7 24.9 - - + +
313A ALA* 3.6 36.1 - - + -
316A LEU* 3.6 18.6 - - + -
337A HIS* 2.9 20.3 + - + +
338A SER* 1.3 77.4 - - - +
340A PHE* 1.3 91.9 + + + +
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LYS* 3.2 32.1 - - - -
162A MET* 3.9 11.0 - - + -
163A TYR* 3.7 25.8 - + + -
166A PHE* 4.0 11.7 - + - -
316A LEU* 4.0 17.0 - - + -
334A ALA 2.9 32.3 - - - -
335A CYS* 3.4 19.1 - - - +
337A HIS* 2.9 10.9 + - + +
339A PHE* 1.3 104.0 - + - +
341A ASP* 1.3 64.1 + - - +
342A GLU* 3.1 3.4 - - - -
343A LEU* 2.8 31.9 + - + +
344A ARG* 3.4 12.4 + - - +
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Residues in contact with ASP 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ALA 4.9 0.7 - - - +
338A SER* 3.2 24.8 + - - +
339A PHE 3.4 0.4 - - - -
340A PHE* 1.3 76.6 - - - +
342A GLU* 1.3 58.1 + - - +
344A ARG* 2.7 59.8 + - - +
345A ASP* 3.4 4.9 + - - +
319B ARG* 2.4 37.6 + - - +
329B LEU* 4.9 3.8 - - - +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 5.5 0.3 - - - +
156A ILE* 3.5 28.8 - - + +
159A LYS* 2.6 44.7 + - + +
340A PHE 3.1 1.0 + - - -
341A ASP* 1.3 77.8 - - - +
343A LEU* 1.3 60.7 + - + +
344A ARG 3.2 0.2 - - - -
345A ASP* 3.5 23.6 + - + +
348A VAL* 3.5 22.2 - - + +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ILE* 4.4 15.3 - - + -
159A LYS* 3.4 45.1 - - + +
160A LEU* 3.4 30.3 - - + +
163A TYR* 3.4 33.0 - - + -
340A PHE* 2.8 25.6 + - + +
342A GLU* 1.3 73.7 - - - +
344A ARG* 1.3 60.2 + - + +
345A ASP 3.2 2.0 + - - +
348A VAL* 4.0 17.8 - - + +
356A THR* 5.3 1.6 + - + -
359A LEU* 3.9 14.0 - - + +
360A PHE* 3.2 18.7 - - + -
381A HIS* 5.4 0.2 + - - -
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Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 4.5 8.3 + - + -
335A CYS 3.0 23.2 + - - -
336A ALA* 3.9 13.9 + - - +
337A HIS 3.1 20.8 + - - -
340A PHE* 3.4 10.8 + - - +
341A ASP* 2.7 44.5 + - - +
343A LEU* 1.3 79.5 - - + +
345A ASP* 1.3 57.6 + - - +
346A PRO* 3.8 1.2 - - - +
360A PHE* 3.5 26.5 - - + -
376A ILE* 3.4 28.9 + - - +
377A LEU* 3.7 13.0 + - - +
379A PRO* 3.5 11.9 - - + +
381A HIS* 3.2 24.5 + - - -
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Residues in contact with ASP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ASP 3.4 4.7 + - - +
342A GLU* 3.5 22.2 - - + +
343A LEU 3.2 1.5 - - - +
344A ARG* 1.3 78.3 - - - +
346A PRO* 1.3 87.2 - - - +
347A ASN* 3.1 31.0 + - - +
348A VAL* 2.9 35.2 + - + +
381A HIS* 3.8 3.2 + - - -
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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