Contacts of the helix formed by residues 1303 - 1309 (chain C) in PDB entry 7C97
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 LYS1303 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1299C ASN 3.9 17.3 + - - +
1300C GLY* 4.5 5.4 - - - +
1301C ARG 3.1 0.6 - - - -
1302C THR* 1.3 80.6 + - - +
1304C MET* 1.3 52.4 + - - +
1305C TYR 3.0 4.5 - - - -
1306C LYS* 2.9 26.2 + - + +
1307C ASN* 2.7 52.7 + - - +
1316C GLU* 4.5 22.2 - - + -
538F GLU* 6.0 3.4 - - - +
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Residues in contact with MET1304 (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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1293C VAL* 3.4 35.9 - - + -
1300C GLY 3.7 8.3 + - - +
1301C ARG 3.1 8.2 + - - +
1303C LYS* 1.3 77.5 - - - +
1305C TYR* 1.3 56.8 + - - +
1307C ASN* 4.1 5.4 - - - +
1308C ILE* 3.0 48.1 - - + +
1314C GLN 3.5 26.5 - - - +
1315C MET* 3.9 13.0 - - + +
349D TYR* 5.0 5.5 + - - +
472D LEU* 3.7 31.4 - - + -
473D THR* 4.0 22.0 - - + +
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Residues in contact with TYR1305 (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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1247C SER* 5.2 0.4 - - - -
1248C THR* 4.2 23.1 - - - -
1301C ARG 3.0 14.0 + - - +
1302C THR 4.3 4.9 - - - +
1303C LYS 3.0 0.6 - - - -
1304C MET* 1.3 78.5 - - - +
1306C LYS* 1.3 60.0 + - + +
1307C ASN 3.5 0.2 - - - -
1308C ILE* 3.9 4.4 - - - +
1309C VAL* 3.0 33.4 + - + +
349D TYR* 4.4 10.1 - - - +
378D LYS* 5.8 0.5 - - - +
379D PRO* 3.7 30.8 - - + +
382D TYR* 3.5 27.2 - - - -
394D ILE* 5.0 0.9 - - + -
530F LEU* 5.7 1.1 - - + +
531F PRO* 3.7 44.4 - - + -
532F LEU* 4.3 17.3 - - + +
535F ALA* 4.5 8.3 - - + -
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Residues in contact with LYS1306 (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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1302C THR* 3.4 22.4 + - - +
1303C LYS* 2.9 30.1 + - + +
1305C TYR* 1.3 78.6 - - + +
1307C ASN* 1.3 66.2 + - - +
1309C VAL* 3.6 9.7 - - + +
1310C ASP* 3.4 26.6 - - - +
531F PRO* 4.6 3.1 - - - -
534F SER* 2.5 50.7 + - - -
535F ALA* 3.9 18.8 - - + +
538F GLU* 4.3 21.1 - - + +
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Residues in contact with ASN1307 (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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1303C LYS* 2.7 38.4 + - - +
1304C MET* 4.5 7.2 - - - +
1306C LYS* 1.3 72.9 - - - +
1308C ILE* 1.3 63.5 - - - +
1310C ASP* 3.2 7.9 + - - +
1312C ASN* 3.0 59.0 + - + +
1314C GLN* 2.9 25.4 + - - +
1315C MET* 4.9 0.2 - - - +
1316C GLU* 3.3 22.6 + - - +
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Residues in contact with ILE1308 (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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1304C MET* 3.0 50.8 + - + +
1305C TYR* 3.8 5.6 + - - +
1306C LYS 3.3 0.2 - - - -
1307C ASN* 1.3 79.3 - - - +
1309C VAL* 1.3 61.9 + - - +
1310C ASP 3.1 1.4 + - - -
1311C GLY* 3.1 12.3 + - - -
1313C HIS* 3.5 31.6 + - + +
349D TYR* 5.6 1.6 - - - +
379D PRO* 3.4 43.5 - - + +
380D PHE* 3.7 24.7 - - + +
383D GLY* 4.9 2.4 - - - -
472D LEU* 4.6 11.9 - - + +
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Residues in contact with VAL1309 (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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1305C TYR* 3.0 38.6 - - + +
1306C LYS* 3.6 15.9 - - + +
1308C ILE* 1.3 75.3 - - - +
1310C ASP* 1.3 76.5 + - - +
1311C GLY 3.5 0.2 - - - -
379D PRO* 3.8 19.3 - - + +
382D TYR* 4.7 11.0 - - + +
383D GLY* 3.4 21.6 - - - +
386D GLU* 5.6 6.0 - - - +
394D ILE* 4.6 18.6 - - + -
535F ALA* 5.6 3.6 - - + -
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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