Contacts of the strand formed by residues 271 - 276 (chain C) in PDB entry 6E7P
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 271 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ALA* 3.3 3.5 - - - -
119C ALA* 3.0 36.7 + - + +
125C LEU* 3.7 24.0 - - + -
225C PHE* 5.8 0.2 - - + -
228C LEU* 5.1 5.6 - - + -
262C PHE* 3.8 26.0 - - + +
263C ASP 3.3 16.2 - - - +
264C ASN* 4.0 24.5 - - + +
270C ARG* 1.3 76.4 - - - +
272C PRO* 1.3 72.5 - - - +
273C ILE* 4.2 1.7 - - - +
144D LEU* 3.7 37.9 - - + -
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Residues in contact with PRO 272 (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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115C ASP 5.8 3.6 - - - +
117C PHE 3.8 8.1 - - - +
118C ALA* 4.3 2.7 - - + -
261C THR 3.6 1.7 - - - +
262C PHE* 3.7 0.3 - - - -
263C ASP* 3.2 46.8 + - + +
264C ASN* 5.4 0.2 - - - -
270C ARG* 3.3 33.7 - - - +
271C ILE* 1.3 92.5 - - - +
273C ILE* 1.3 62.4 + - - +
274C SER* 5.0 5.6 - - - +
96D GLU* 5.1 2.5 - - - +
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Residues in contact with ILE 273 (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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106C LEU* 3.7 30.3 - - + +
114C ASP 4.5 10.0 - - - +
117C PHE* 3.3 45.5 + - + +
118C ALA 4.5 4.0 - - - +
119C ALA* 4.2 20.9 - - + -
128C ALA* 4.4 10.1 - - + -
260C ILE* 4.8 1.6 - - + -
261C THR 3.5 4.3 - - - +
262C PHE* 3.7 38.1 - - + -
271C ILE 4.2 5.6 - - - +
272C PRO* 1.3 80.3 - - - +
274C SER* 1.3 69.9 + - - +
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Residues in contact with SER 274 (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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106C LEU* 4.6 5.0 - - - +
260C ILE* 3.6 11.1 - - - +
261C THR* 3.2 40.5 + - - +
263C ASP* 6.0 1.4 - - - +
272C PRO* 5.0 5.7 - - - +
273C ILE* 1.3 81.7 + - - +
275C LEU* 1.3 67.0 + - - +
276C GLU* 5.0 8.5 - - - -
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Residues in contact with LEU 275 (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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486B ARG* 4.2 2.9 + - - -
98C THR* 4.7 7.0 - - - +
101C PHE* 4.3 29.4 - - + +
102C ARG* 3.9 52.4 + - + +
105C PHE* 4.6 2.2 - - + -
106C LEU* 4.6 11.2 - - + -
258C VAL* 4.3 14.8 - - + -
259C LEU 3.4 6.1 - - - -
260C ILE* 4.1 21.3 - - + -
274C SER* 1.3 79.0 - - - +
276C GLU* 1.3 88.6 + - - +
277C THR* 4.4 11.9 - - + -
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Residues in contact with GLU 276 (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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486B ARG* 2.5 47.1 + - - +
257C SER 3.3 4.2 - - - +
258C VAL* 3.3 2.6 - - - -
259C LEU* 3.2 49.6 + - + +
261C THR* 5.5 2.5 - - - +
274C SER* 5.0 7.3 - - - -
275C LEU* 1.3 83.7 + - - +
277C THR* 1.3 71.1 + - - +
278C GLN* 4.4 14.1 + - - +
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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