Contacts of the helix formed by residues 300 - 310 (chain C) in PDB entry 2GD4
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 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C THR* 3.9 8.8 - - - +
298C GLU 3.3 17.5 - - - +
299C LEU* 1.3 75.4 - - - +
301C PRO* 1.3 73.5 - - - +
302C GLU* 2.6 31.6 + - + +
303C VAL* 3.2 20.9 - - + +
304C LEU* 3.1 21.3 + - - +
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Residues in contact with PRO 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C SER* 5.0 4.0 - - - +
57C ARG* 4.3 28.3 - - + +
60C THR* 3.3 29.4 - - + +
61C THR* 5.9 0.2 - - - +
300C THR* 1.3 94.0 - - - +
302C GLU* 1.3 78.4 + - - +
304C LEU* 3.1 18.8 + - + +
305C GLN* 3.2 12.0 + - - +
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Residues in contact with GLU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C THR* 2.6 22.9 + - + +
301C PRO* 1.3 92.4 - - - +
303C VAL* 1.3 55.1 + - - +
305C GLN* 3.1 22.3 - - - +
306C GLU* 3.6 5.2 + - - +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C GLU* 4.2 6.3 - - + +
299C LEU* 4.2 13.7 - - + -
300C THR* 3.2 41.6 + - + +
302C GLU* 1.3 76.1 - - - +
304C LEU* 1.3 64.6 + - - +
305C GLN 3.0 2.0 - - - -
306C GLU* 3.8 21.3 - - + +
307C TRP* 3.3 41.8 + - + +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C SER* 5.1 4.5 - - - +
60C THR* 4.6 13.0 - - + -
299C LEU* 5.2 2.0 - - + -
300C THR 3.1 12.8 + - - +
301C PRO* 3.1 12.3 + - + +
303C VAL* 1.3 78.6 - - - +
305C GLN* 1.3 64.4 + - - +
307C TRP* 3.6 15.8 - - + +
308C LEU* 3.5 35.5 + - + +
411C PHE* 3.1 45.3 - - + -
420C ILE* 3.2 35.9 - - + -
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Residues in contact with GLN 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C PRO 3.2 8.2 + - - +
302C GLU* 3.1 16.2 - - - +
304C LEU* 1.3 78.1 - - - +
306C GLU* 1.3 58.9 + - - +
308C LEU* 2.9 6.4 + - - +
309C ASP* 2.5 88.0 + - + +
418C ASN* 4.8 11.1 + - - -
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ARG* 5.0 6.3 + - - +
263C VAL* 3.7 31.3 - - + +
264C ALA* 4.3 10.7 + - - +
265C GLU* 5.2 1.4 + - - +
302C GLU 3.6 5.0 + - - +
303C VAL* 3.6 25.5 + - - +
304C LEU 3.5 0.2 - - - -
305C GLN* 1.3 80.0 - - - +
307C TRP* 1.3 68.2 + - + +
308C LEU 3.0 2.3 + - - -
309C ASP* 3.7 10.3 + - - -
310C GLU* 4.0 10.7 + - - +
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Residues in contact with TRP 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ARG* 4.5 3.3 - - - +
263C VAL* 4.0 16.8 - - + +
265C GLU* 6.0 0.4 - - - -
267C THR* 4.5 13.4 + - + -
269C VAL* 2.9 50.8 - - + +
284C ILE* 3.5 46.2 - - + -
295C VAL* 4.2 20.6 - - + -
298C GLU* 5.7 3.1 - - + -
299C LEU* 3.4 34.5 - - + -
303C VAL* 3.3 31.7 + - + +
304C LEU* 3.6 17.3 - - + +
305C GLN 3.2 0.6 - - - -
306C GLU* 1.3 80.2 - - + +
308C LEU* 1.3 60.9 + - + +
311C LEU* 3.6 7.6 - - - +
409C LEU* 4.1 8.7 - - + -
411C PHE* 3.6 15.9 - + - -
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C VAL* 4.0 2.9 - - + -
282C VAL* 3.9 36.1 - - + -
284C ILE* 5.5 0.4 - - + -
304C LEU* 3.5 28.0 + - + +
305C GLN* 2.9 10.7 + - - +
307C TRP* 1.3 86.7 - - + +
309C ASP* 1.3 54.1 + - - +
310C GLU 2.5 20.5 + - - -
311C LEU* 3.2 29.9 + - + +
411C PHE* 6.4 0.4 - - + -
413C ARG* 2.8 42.2 - - - +
418C ASN* 4.5 8.5 - - - +
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Residues in contact with ASP 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C GLN* 2.5 55.4 + - + +
306C GLU* 4.2 6.3 - - - +
308C LEU* 1.3 70.8 - - - +
310C GLU* 1.3 59.4 + - + +
311C LEU 4.1 0.7 + - - -
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Residues in contact with GLU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ARG* 3.2 41.6 - - - +
306C GLU 4.0 5.9 + - - +
307C TRP 4.5 0.2 - - - +
308C LEU 2.5 8.5 + - - +
309C ASP* 1.3 80.2 - - + +
311C LEU* 1.3 57.7 + - - +
312C GLU* 5.5 2.5 - - + -
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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