Contacts of the helix formed by residues 306 - 312 (chain E) in PDB entry 6GL7
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 306 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D GLY 3.9 0.2 - - - -
328D SER 3.2 9.6 - - - +
329D GLY* 3.0 25.6 - - - +
330D ASN* 3.5 9.0 - - + +
264E ASP* 5.0 1.6 - - - +
303E VAL 2.7 27.1 + - - +
304E VAL 4.0 3.4 - - - -
305E PRO* 1.3 78.4 - - + +
307E SER* 1.3 64.6 + - - +
308E GLY* 4.3 4.0 - - - +
309E GLU* 3.5 25.8 + - + +
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Residues in contact with SER 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ASN* 4.8 4.9 + - - -
253D ASP* 4.3 17.2 + - - -
326D ARG 5.2 1.1 - - - -
327D GLY* 2.2 44.8 + - - -
328D SER* 4.8 0.5 - - - -
304E VAL 5.3 0.2 - - - -
306E ALA* 1.3 69.2 - - - +
308E GLY* 1.3 65.9 + - - +
309E GLU 3.2 0.7 + - - -
310E LEU* 3.3 5.7 + - - +
311E VAL* 3.1 34.4 + - - +
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Residues in contact with GLY 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D SER 5.3 0.8 + - - -
306E ALA* 3.3 3.2 - - - +
307E SER* 1.3 84.7 + - - +
309E GLU* 1.3 61.2 + - - +
311E VAL* 4.2 7.9 - - - -
312E ARG* 3.0 52.0 + - - +
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Residues in contact with GLU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ASN* 3.4 23.6 + - - +
264E ASP* 5.7 5.4 - - + +
266E ASP* 5.2 6.1 - - - +
302E ASP* 4.2 14.2 - - - +
303E VAL* 3.7 23.3 - - + -
306E ALA* 3.5 23.0 + - + +
307E SER 3.2 1.6 - - - -
308E GLY* 1.3 77.1 - - - +
310E LEU* 1.3 58.0 + - - +
312E ARG* 2.6 29.7 + - - +
313E ARG* 3.5 13.0 + - - +
360E ARG* 3.7 32.6 + - - -
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Residues in contact with LEU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E VAL* 4.1 32.2 + - + +
307E SER* 3.3 6.5 + - - +
308E GLY 3.2 0.2 - - - -
309E GLU* 1.3 77.9 - - - +
311E VAL* 1.3 60.4 + - + +
313E ARG 2.5 31.3 - - - +
314E TYR* 3.2 38.0 - - + +
333E HIS* 4.1 21.3 - - + +
334E TRP* 3.6 38.6 - - + +
336E ASN* 4.0 17.9 - - - +
358E LEU 5.4 0.2 - - - +
359E ASN 4.8 4.3 - - - +
360E ARG* 4.9 3.6 - - - -
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Residues in contact with VAL 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E SER* 3.1 27.5 + - - +
308E GLY* 4.1 6.7 - - - +
310E LEU* 1.3 74.8 - - + +
312E ARG* 1.3 68.4 + - + +
313E ARG 3.3 0.5 + - - -
314E TYR* 3.8 18.7 - - + -
334E TRP* 6.1 7.0 - - + -
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Residues in contact with ARG 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D ASN* 5.4 0.2 - - - +
308E GLY* 3.0 34.6 + - - +
309E GLU* 2.6 44.0 + - - +
311E VAL* 1.3 80.9 - - + +
313E ARG* 1.3 74.6 + - + +
314E TYR* 5.1 0.4 - - - -
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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