Contacts of the helix formed by residues 306 - 312 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C GLY 3.7 4.0 - - - -
328C SER 3.8 15.0 - - - +
329C GLY* 3.8 7.4 - - - -
330C ASN* 4.0 13.2 - - + +
264F ASP* 5.0 2.2 - - - +
303F VAL 2.7 26.4 + - - +
304F VAL 3.9 3.3 - - - +
305F PRO* 1.3 80.3 - - + +
307F SER* 1.3 65.2 + - - +
308F GLY* 4.3 4.3 - - - +
309F GLU* 3.5 25.8 + - + +
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Residues in contact with SER 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ASN* 5.7 1.8 + - - -
253C ASP* 4.2 23.3 + - - -
327C GLY* 2.9 22.3 + - - -
328C SER* 4.7 1.3 + - - -
304F VAL 5.3 0.4 - - - -
306F ALA* 1.3 72.7 - - - +
308F GLY* 1.3 66.7 + - - +
309F GLU 3.2 0.3 + - - -
310F LEU* 3.3 5.8 + - - +
311F VAL* 3.1 33.9 + - - +
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Residues in contact with GLY 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ALA* 3.3 3.4 - - - +
307F SER* 1.3 84.2 + - - +
309F GLU* 1.3 61.3 + - - +
311F VAL* 4.2 8.1 - - - -
312F ARG* 3.0 51.7 + - - +
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Residues in contact with GLU 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ASN* 3.9 17.2 + - - +
264F ASP* 5.7 6.5 - - + +
266F ASP* 5.2 6.4 - - - +
302F ASP* 4.2 14.5 - - - +
303F VAL* 3.7 23.6 - - + -
306F ALA* 3.7 23.2 - - + +
307F SER 3.2 1.4 - - - -
308F GLY* 1.3 76.5 - - - +
310F LEU* 1.3 60.7 + - - +
312F ARG* 2.6 28.4 + - - +
313F ARG* 3.5 12.5 + - - +
360F ARG* 3.7 32.4 + - - -
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Residues in contact with LEU 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F VAL* 4.1 34.2 + - + +
304F VAL* 6.3 0.2 - - - -
307F SER* 3.3 7.2 + - - +
309F GLU* 1.3 78.1 - - - +
311F VAL* 1.3 61.4 + - + +
313F ARG 2.5 31.4 - - - +
314F TYR* 3.2 37.2 - - + +
333F HIS* 4.1 20.9 - - + +
334F TRP* 3.6 37.9 - - + +
336F ASN* 4.0 17.7 - - - +
358F LEU 5.4 0.4 - - - +
359F ASN 4.8 4.9 - - - +
360F ARG* 4.9 2.7 - - - -
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Residues in contact with VAL 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F SER* 3.1 26.9 + - - +
308F GLY* 4.1 6.1 - - - +
310F LEU* 1.3 73.3 - - + +
312F ARG* 1.3 69.3 + - + +
313F ARG 3.3 0.3 + - - -
314F TYR* 3.8 18.7 - - - -
334F TRP* 6.1 7.0 - - + -
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Residues in contact with ARG 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C ASN* 5.6 0.2 - - - +
308F GLY* 3.0 36.7 + - - +
309F GLU* 2.6 44.4 + - - +
311F VAL* 1.3 80.0 - - + +
313F ARG* 1.3 75.3 + - + +
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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