Contacts of the helix formed by residues 300 - 313 (chain C) in PDB entry 7A62
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 PRO 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C HIS* 6.5 0.2 - - + -
77C ARG* 5.0 13.9 - - - +
120C LEU* 3.9 9.6 - - + -
127C ALA* 3.7 31.2 - - + -
131C LEU* 5.0 3.4 - - + -
268C SER* 5.2 1.6 - - - +
299C MET* 1.3 87.6 - - + +
301C PRO* 1.3 75.8 - - + +
302C ALA* 4.5 3.4 - - + +
303C HIS* 2.9 48.6 + - + +
304C ARG 2.9 9.9 + - - -
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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
----------------------------------------------------------
118C LEU 3.3 26.9 - - - +
119C GLU* 3.7 31.6 - - + +
120C LEU* 4.7 1.6 - - + -
299C MET 3.4 2.0 - - - +
300C PRO* 1.3 84.6 - - + +
302C ALA* 1.3 64.7 + - + +
304C ARG* 3.1 29.5 + - - +
305C ASN* 2.9 33.5 + - - +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA 5.2 0.4 - - - +
15C TYR* 3.4 28.6 - - - +
16C HIS* 3.8 29.6 - - + -
300C PRO* 3.2 2.9 - - + -
301C PRO* 1.3 81.5 - - + +
303C HIS* 1.3 60.7 + - + +
305C ASN* 3.5 11.7 + - - +
306C PHE* 3.1 25.1 + - - +
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Residues in contact with HIS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR 3.2 18.2 - - - -
16C HIS* 2.8 24.8 + - - +
17C ILE* 4.2 1.8 - - + -
23C PHE* 3.2 63.4 - + + +
77C ARG* 6.1 2.2 - - - -
131C LEU* 4.7 2.1 - - + +
268C SER* 4.1 12.4 + - - +
299C MET* 4.7 1.8 - - + -
300C PRO* 2.9 39.8 + - + +
302C ALA* 1.3 77.6 - - + +
304C ARG* 1.3 66.8 + - - +
306C PHE* 3.3 6.3 + - - +
307C LEU* 3.1 28.7 + - - +
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Residues in contact with ARG 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLU* 3.0 33.7 + - - +
120C LEU* 4.5 0.2 - - - +
296C ARG* 3.1 38.3 + - + +
297C ARG* 3.2 25.9 + - - +
299C MET* 2.6 32.2 + - + +
300C PRO 2.9 10.2 + - - +
301C PRO* 3.1 27.4 + - - +
303C HIS* 1.3 78.3 - - - +
305C ASN* 1.3 66.4 + - - +
307C LEU* 3.3 10.7 + - - +
308C CYS* 3.2 26.4 + - - -
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Residues in contact with ASN 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 4.1 14.9 - - + -
301C PRO* 2.9 28.3 + - - +
302C ALA* 3.7 9.5 - - - +
304C ARG* 1.3 76.3 - - - +
306C PHE* 1.3 60.4 + - - +
308C CYS* 3.0 9.6 + - - +
309C SER* 2.8 29.8 + - - -
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Residues in contact with PHE 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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12C SER* 4.7 11.4 - - - -
15C TYR* 3.6 36.7 - + + -
17C ILE* 3.5 32.5 - - + -
23C PHE* 4.1 13.0 - + - -
178C ILE* 4.6 6.1 - - + -
181C ILE* 4.4 17.0 - - + -
272C CYS* 4.1 16.6 - - - -
302C ALA 3.1 16.7 + - - +
303C HIS* 3.7 6.7 - - - +
304C ARG 3.3 0.2 - - - -
305C ASN* 1.3 76.4 - - - +
307C LEU* 1.3 69.0 + - + +
309C SER* 3.0 20.5 + - - -
310C LEU* 3.0 43.6 + - + +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 5.2 0.4 - - + -
268C SER* 4.3 8.5 - - - +
271C GLN* 4.1 12.6 - - + +
272C CYS* 3.7 37.7 - - + +
275C VAL* 4.0 7.6 - - + +
296C ARG* 3.7 37.2 - - - +
299C MET* 3.9 26.7 - - + -
303C HIS 3.1 14.0 + - - +
304C ARG* 3.7 7.4 - - - +
305C ASN 3.3 0.2 - - - -
306C PHE* 1.3 86.3 - - + +
308C CYS* 1.3 60.6 + - - +
310C LEU* 3.7 7.7 + - + +
311C GLU* 3.2 25.9 + - - +
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Residues in contact with CYS 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLN* 5.6 4.7 - - - -
296C ARG* 4.7 12.1 - - - -
304C ARG* 3.2 16.9 + - - +
305C ASN* 3.0 11.9 + - - +
307C LEU* 1.3 75.4 - - - +
309C SER* 1.3 66.0 - - - +
311C GLU* 3.1 16.8 + - - +
312C SER* 2.9 20.6 + - - +
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Residues in contact with SER 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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15C TYR* 3.6 28.0 + - - -
305C ASN 2.8 14.0 + - - -
306C PHE* 3.0 13.7 + - - -
308C CYS* 1.3 76.9 - - - +
310C LEU* 1.3 71.9 + - - +
312C SER* 3.0 16.6 + - - -
313C ASN* 3.1 23.0 + - - +
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Residues in contact with LEU 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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181C ILE* 3.9 18.4 - - + -
185C PHE* 3.6 31.7 - - + -
272C CYS* 3.8 28.5 - - - +
275C VAL* 3.5 21.6 - - + +
276C LEU* 4.5 7.8 - - + +
306C PHE* 3.0 44.6 + - + +
307C LEU* 3.9 3.6 - - - +
309C SER* 1.3 85.0 + - - +
311C GLU* 1.3 64.1 + - - +
312C SER 3.0 1.2 + - - -
313C ASN* 3.3 23.5 + - - +
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Residues in contact with GLU 311 (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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275C VAL* 3.5 21.3 - - + +
280C GLN* 6.2 0.3 - - - +
282C THR* 3.5 24.1 + - - +
293C GLN* 5.4 1.1 - - - +
296C ARG* 3.4 28.7 + - - -
307C LEU 3.2 10.3 + - - +
308C CYS* 3.1 14.9 + - - +
310C LEU* 1.3 78.6 - - - +
312C SER* 1.3 57.8 + - - +
313C ASN 4.2 3.9 - - - +
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C CYS* 2.9 14.4 + - - +
309C SER* 3.0 11.2 + - - -
310C LEU 3.0 1.2 - - - -
311C GLU* 1.3 77.4 - - - +
313C ASN* 1.3 69.4 + - - +
314C PRO* 4.5 0.7 - - - +
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Residues in contact with ASN 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C PHE* 3.5 46.7 - - + -
309C SER* 3.1 20.9 + - - +
310C LEU* 3.3 15.8 + - - +
311C GLU 4.2 4.0 - - - +
312C SER* 1.3 85.2 - - - +
314C PRO* 1.3 78.1 - - + +
315C SER* 3.6 1.4 + - - -
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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