Contacts of the strand formed by residues 346 - 354 (chain A) in PDB entry 2C11
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 GLY 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A LEU* 3.4 5.2 - - - -
342A GLY* 2.6 41.8 + - - -
344A PHE 3.3 1.6 - - - -
345A SER* 1.3 84.1 + - - +
347A PRO* 1.3 75.5 - - - +
348A ARG* 3.5 1.4 + - - -
391A MET* 3.7 15.0 - - - -
392A GLY 3.9 2.7 - - - -
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Residues in contact with PRO 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A GLY 3.8 1.6 - - - +
341A LEU* 3.3 21.3 - - + -
346A GLY* 1.3 82.4 - - - +
348A ARG* 1.3 58.5 + - - +
364A SER* 3.4 1.0 - - - -
365A LEU* 2.8 50.9 + - + -
391A MET* 4.7 0.9 - - + -
429A PHE* 5.9 1.1 - - + -
464A SER* 4.2 7.0 - - - +
466A SER* 5.1 0.7 - - - +
475A TRP* 3.3 44.6 - - + +
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE 4.9 2.2 + - - -
62A ASP* 3.0 22.2 + - - +
100A GLU* 3.2 27.1 + - - +
101A LEU* 4.1 27.5 + - - +
103A LEU* 4.0 23.8 - - - +
339A PHE* 3.4 0.9 - - - +
340A GLY* 3.0 40.1 + - - +
341A LEU 3.8 13.1 + - - +
342A GLY* 3.4 16.2 - - - +
345A SER* 4.7 8.0 + - - -
346A GLY 4.2 1.1 - - - +
347A PRO* 1.3 74.3 - - - +
349A ILE* 1.3 67.0 + - - +
350A PHE* 3.7 27.8 - - + -
363A ILE 3.5 6.7 - - - -
364A SER* 3.4 20.4 - - - -
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PHE* 3.6 19.5 - - + -
338A SER 3.2 11.0 - - - +
339A PHE* 3.8 9.4 - - + -
348A ARG* 1.3 81.3 - - - +
350A PHE* 1.3 68.3 + - - +
352A VAL* 3.6 27.4 - - + -
362A GLU* 3.0 4.9 - - - +
363A ILE* 2.7 50.7 + - + +
462A VAL* 4.3 4.7 - - + -
477A THR* 4.0 22.7 - - + +
479A PHE* 3.5 29.6 - - + -
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Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.2 59.0 - + + -
103A LEU* 3.7 32.8 - - + -
337A PHE* 3.5 3.1 - - - +
338A SER* 2.6 38.3 + - - +
339A PHE 5.5 2.2 - - - -
348A ARG* 3.7 34.3 - - + -
349A ILE* 1.3 76.3 - - - +
351A ASP* 1.3 69.2 + - - +
352A VAL* 3.4 4.6 + - - -
361A TYR* 3.2 12.1 - + - +
362A GLU* 3.3 46.4 - - + -
364A SER* 5.6 0.2 - - - -
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 4.6 5.1 - - + -
113A LEU* 3.1 29.7 - - + +
329A ARG* 3.4 23.9 + - - +
336A THR 3.0 13.7 - - - +
337A PHE* 3.1 5.2 - - - -
350A PHE* 1.3 78.6 - - + +
352A VAL* 1.3 56.9 + - - +
353A ARG* 2.8 28.9 + - - +
358A ARG* 2.7 31.9 + - - +
360A VAL 3.6 6.1 - - - -
361A TYR* 2.9 14.4 + - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A TRP* 3.6 15.5 - - + -
336A THR 3.2 5.2 - - - +
337A PHE* 3.9 1.6 - - + -
349A ILE* 3.6 31.6 - - + +
350A PHE* 4.2 2.0 - - - +
351A ASP* 1.3 72.3 - - - +
353A ARG* 1.3 60.4 + - - +
357A GLU 3.5 0.2 - - - +
358A ARG* 3.0 3.3 - - - +
359A LEU* 2.8 30.8 + - + +
360A VAL* 3.1 35.5 + - + +
363A ILE* 4.7 3.1 - - + -
479A PHE* 3.5 27.4 - - + -
485A ILE* 3.5 18.2 - - + -
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Residues in contact with ARG 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.7 24.4 + - - +
114A ASP* 4.3 6.5 - - - +
329A ARG* 4.7 2.6 - - - +
334A LEU 3.6 0.2 - - - +
335A TRP* 3.5 5.7 - - - -
336A THR* 2.7 56.2 + - + +
351A ASP* 2.8 35.5 + - - +
352A VAL* 1.3 74.1 - - - +
354A PHE* 1.3 61.1 + - - +
355A GLN 3.4 3.3 + - - -
356A GLY* 3.7 29.2 + - - +
357A GLU 3.0 4.0 - - - -
358A ARG* 3.0 34.7 - - - +
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Residues in contact with PHE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU* 3.4 32.8 - - + -
335A TRP* 3.4 48.6 - + + -
352A VAL 4.2 0.8 - - - -
353A ARG* 1.3 69.7 - - - +
355A GLN* 1.3 88.1 + - - +
357A GLU* 2.8 23.8 + - + +
359A LEU* 4.1 22.9 - - + +
480A HIS 3.9 1.3 - - - -
481A PRO 3.6 17.9 - - - -
483A GLY* 3.6 13.2 - - - -
711A PHE* 3.9 20.7 - + + -
715A PRO* 3.8 28.5 - - + -
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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