Contacts of the strand formed by residues 346 - 354 (chain D) in PDB entry 2C10
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341D LEU* 3.7 3.4 - - - -
342D GLY* 2.8 41.3 + - - -
344D PHE 3.4 2.2 - - - -
345D SER* 1.3 82.1 + - - +
347D PRO* 1.3 74.0 - - - +
348D ARG* 3.7 4.7 + - - +
364D SER* 5.5 0.2 - - - -
365D LEU 4.8 0.7 - - - +
391D MET* 3.6 12.6 - - - -
392D GLY 3.9 3.1 - - - -
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Residues in contact with PRO 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D GLY 3.6 10.3 - - - +
341D LEU* 3.3 16.1 - - + -
346D GLY* 1.3 83.7 - - - +
348D ARG* 1.3 57.6 + - - +
364D SER* 3.5 0.3 - - - -
365D LEU* 2.8 46.8 + - + -
391D MET* 4.6 2.9 - - + +
429D PHE* 5.7 1.8 - - + -
464D SER* 4.0 8.3 - - - +
466D SER* 5.3 0.2 - - - +
475D TRP* 3.5 43.3 - - + +
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Residues in contact with ARG 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE 5.2 1.8 + - - -
62D ASP* 2.7 28.5 + - - -
100D GLU* 4.7 6.7 + - - -
101D LEU* 4.2 24.9 + - - +
103D LEU* 3.9 29.4 - - - +
339D PHE* 3.5 1.0 - - - +
340D GLY* 3.2 38.5 + - - +
341D LEU 3.8 6.9 + - - +
342D GLY* 3.6 27.2 - - - +
345D SER* 5.0 5.0 + - - -
346D GLY 4.2 2.5 - - - +
347D PRO* 1.3 77.5 - - - +
349D ILE* 1.3 69.8 + - - +
350D PHE* 3.6 27.1 - - + -
362D GLU* 5.6 0.2 - - - -
363D ILE 3.3 6.5 - - - +
364D SER* 3.5 20.0 - - - -
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Residues in contact with ILE 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D PHE* 4.0 18.4 - - + -
338D SER 3.3 4.3 - - - +
339D PHE* 4.3 14.4 - - + -
348D ARG* 1.3 80.9 - - - +
350D PHE* 1.3 68.2 + - - +
352D VAL* 3.3 29.3 - - + +
362D GLU* 3.4 4.0 - - - +
363D ILE* 2.7 44.7 + - + +
462D VAL* 4.8 8.3 - - + -
477D THR* 3.5 43.1 - - + +
479D PHE* 3.7 14.1 - - + -
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Residues in contact with PHE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 3.5 57.9 - + + -
103D LEU* 3.6 32.8 - - + -
337D PHE* 3.5 1.6 - - - +
338D SER* 2.7 37.9 + - - +
339D PHE 5.9 1.8 - - - -
348D ARG* 3.6 34.3 - - + -
349D ILE* 1.3 78.0 - - - +
351D ASP* 1.3 69.7 + - - +
352D VAL* 3.3 4.1 + - - -
361D TYR* 3.4 21.3 - + - +
362D GLU* 3.5 37.9 - - + -
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Residues in contact with ASP 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 4.1 17.0 - - + -
113D LEU* 3.9 12.5 - - + +
329D ARG* 3.1 25.9 + - - +
336D THR 3.1 11.4 - - - +
337D PHE* 3.5 4.2 - - - -
350D PHE* 1.3 74.6 - - - +
352D VAL* 1.3 62.8 + - - +
353D ARG* 2.8 42.7 + - - +
358D ARG* 3.2 26.1 + - - +
360D VAL 3.5 6.4 + - - -
361D TYR* 3.0 15.3 + - + +
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Residues in contact with VAL 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D TRP* 3.7 23.8 - - + -
336D THR 3.2 7.4 - - - +
337D PHE* 3.9 4.3 - - + -
349D ILE* 3.3 33.7 - - + -
350D PHE 4.2 2.2 - - - +
351D ASP* 1.3 71.5 - - - +
353D ARG* 1.3 61.1 + - - +
358D ARG* 3.2 4.7 - - - +
359D LEU* 2.8 27.5 + - + -
360D VAL* 3.1 32.0 + - + +
363D ILE* 5.5 2.5 - - + -
479D PHE* 3.6 26.5 - - + -
485D ILE* 4.2 7.0 - - + -
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Residues in contact with ARG 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.1 25.3 + - - +
329D ARG* 4.5 6.7 - - - +
334D LEU 3.7 0.3 - - - +
335D TRP* 3.4 10.8 - - - -
336D THR* 2.6 51.4 + - + +
351D ASP* 2.8 40.7 + - - +
352D VAL* 1.3 78.8 - - - +
354D PHE* 1.3 58.8 + - - +
355D GLN 4.0 0.4 + - - -
356D GLY* 3.8 27.3 + - - +
357D GLU 3.0 9.9 - - - +
358D ARG* 3.7 29.4 - - - +
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Residues in contact with PHE 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D LEU* 3.3 21.8 - - + -
335D TRP* 3.4 47.1 - + + -
353D ARG* 1.3 70.9 - - - +
355D GLN* 1.3 96.9 + - - +
356D GLY 3.0 0.4 - - - -
357D GLU* 2.7 28.4 + - - +
359D LEU* 3.8 15.3 - - + +
480D HIS 4.1 1.6 - - - -
481D PRO 3.8 19.3 - - - -
483D GLY* 3.8 19.3 - - - -
710D PHE* 6.2 0.2 - - + -
711D PHE* 3.5 34.6 - + - -
715D PRO* 3.7 14.8 - - + -
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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