Contacts of the helix formed by residues 313 - 318 (chain C) in PDB entry 6RQT
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 ILE 313 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C MET* 3.6 28.0 - - + +
75C VAL* 3.8 20.2 - - + -
221C PRO* 3.7 29.6 - - + +
222C VAL* 3.7 30.5 - - + -
302C VAL* 5.6 4.5 - - + -
308C MET* 4.4 14.6 - - + -
309C THR 3.9 13.7 - - - +
310C PRO* 4.1 12.1 + - + +
312C GLU* 1.3 74.2 - - - +
314C PHE* 1.3 62.4 + - - +
315C PHE 3.2 2.0 - - - -
316C LYS* 2.9 22.6 + - + -
317C SER 3.0 12.2 + - - +
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Residues in contact with PHE 314 (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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47C LEU* 6.0 0.2 - - + -
54C PHE* 5.6 6.5 - + + -
71C MET* 3.7 19.1 - - + -
310C PRO 3.5 15.9 + - - +
311C GLU* 3.2 34.3 - - - -
312C GLU* 3.8 2.5 - - - -
313C ILE* 1.3 80.8 - - - +
315C PHE* 1.3 110.8 + + + +
317C SER* 3.4 0.2 + - - -
318C VAL* 3.2 37.4 + - + +
135K PHE* 3.5 28.9 - + + -
139K ILE* 4.2 28.7 - - + -
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Residues in contact with PHE 315 (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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312C GLU 3.9 6.7 + - - +
313C ILE 3.2 0.4 - - - -
314C PHE* 1.3 113.7 - + + +
316C LYS* 1.3 70.5 + - + +
318C VAL* 5.0 5.4 - - + -
319C ARG* 3.2 72.9 - - + +
131K VAL 4.5 2.2 - - - -
132K GLU* 4.1 14.8 - - + -
135K PHE* 4.4 12.6 - + - -
136K THR* 4.2 23.6 - - + -
139K ILE* 5.8 2.2 - - + -
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Residues in contact with LYS 316 (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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70C ILE* 4.4 3.6 - - - +
75C VAL* 3.9 26.4 - - + +
76C PRO* 4.8 11.8 - - + +
109C ASP* 5.5 2.1 + - - -
110C PRO* 5.8 9.2 - - + -
111C ASP* 5.1 11.0 - - - +
308C MET* 4.7 11.2 - - + -
312C GLU* 3.4 40.7 + - - +
313C ILE* 2.9 14.3 + - + +
315C PHE* 1.3 88.0 + - - +
317C SER* 1.3 59.0 + - - +
318C VAL 3.4 1.1 - - - -
319C ARG* 4.3 3.6 - - - +
320C ILE* 3.3 29.4 - - + +
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Residues in contact with SER 317 (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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67C PHE* 4.4 13.3 + - - -
70C ILE* 3.4 49.7 + - - +
71C MET* 3.3 35.9 - - - +
313C ILE 3.0 4.2 + - - -
314C PHE 3.4 5.5 + - - -
316C LYS* 1.3 77.4 - - - +
318C VAL* 1.3 66.8 + - - +
321C LEU* 3.4 14.7 - - - +
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Residues in contact with VAL 318 (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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67C PHE* 3.6 30.5 - - + -
314C PHE* 3.2 19.8 + - + +
315C PHE* 4.8 4.0 - - + -
317C SER* 1.3 82.7 - - - +
319C ARG* 1.3 64.2 + - + +
320C ILE 3.2 2.5 - - - -
321C LEU* 3.0 3.6 + - - +
322C LYS* 2.5 38.8 + - + +
128K CYS* 3.7 35.8 - - + +
131K VAL* 5.1 14.1 - - + +
132K GLU* 5.1 6.5 - - + +
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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