Contacts of the strand formed by residues 436 - 440 (chain A) in PDB entry 2C17
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 VAL 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395 HEM 6.2 5.6 - - + -
65A ILE* 5.9 3.1 - - + -
155A ASN* 4.7 3.3 - - - +
254A GLY 5.5 0.2 - - - +
255A ALA* 4.1 20.9 - - + +
258A GLU* 3.6 37.6 - - + +
259A THR* 3.7 33.2 - - + +
319A VAL* 3.5 12.6 - - + +
320A ALA* 5.6 0.7 - - - -
321A PRO* 5.3 1.6 - - + -
434A LYS* 3.4 18.5 - - - +
435A VAL* 1.3 82.7 - - + +
437A PHE* 1.3 65.4 + - - +
438A LEU* 3.5 5.9 + - - +
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Residues in contact with PHE 437 (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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3A HIS* 5.4 1.3 - - + -
4A ASN* 3.4 17.5 - - - -
258A GLU 5.1 0.2 - - - +
262A SER* 2.5 31.4 + - - -
266A TRP* 3.3 38.9 - + + -
317A ARG* 3.3 26.9 - - - -
318A PRO 4.4 1.3 - - - +
319A VAL* 2.8 22.8 + - - +
320A ALA 4.5 3.4 - - - +
321A PRO* 4.9 6.9 - - + -
350A TRP* 3.8 19.1 - + - -
431A GLY* 3.9 8.3 - - - -
432A ILE 3.5 14.4 - - - -
433A PRO* 3.6 36.8 - - + -
434A LYS 4.0 3.7 + - - +
436A VAL* 1.3 71.6 - - - +
438A LEU* 1.3 76.3 + - - +
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Residues in contact with LEU 438 (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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122A PHE* 4.1 30.5 - - + -
125A PHE* 6.2 0.9 - - + -
152A GLN* 6.4 0.2 - - + -
258A GLU* 3.4 43.1 - - + +
261A THR* 4.0 15.7 - - + -
262A SER* 3.7 31.4 - - - +
265A LYS* 6.0 1.1 - - + -
431A GLY* 3.2 4.0 - - - -
432A ILE* 2.8 44.4 + - + +
434A LYS* 4.2 13.0 - - + +
436A VAL 3.5 5.1 + - - +
437A PHE* 1.3 81.9 - - - +
439A ILE* 1.3 68.0 + - + +
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Residues in contact with ILE 439 (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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120A ILE* 5.1 2.9 - - - +
122A PHE* 3.5 22.7 - - - -
262A SER* 3.3 47.3 - - - +
265A LYS* 4.1 18.3 - - + +
266A TRP* 3.5 42.2 - - + +
429A LEU* 3.9 9.4 - - + -
430A GLU 3.6 9.4 - - - +
431A GLY* 3.9 0.7 - - - -
432A ILE* 3.8 5.0 - - - +
438A LEU* 1.3 78.6 - - + +
440A ASP* 1.3 72.7 + - - +
442A PHE* 3.6 24.9 - - + -
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Residues in contact with ASP 440 (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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1A HIS* 5.8 2.4 - - - -
120A ILE* 4.0 13.3 - - - +
122A PHE* 6.0 0.2 - - - -
425A GLN* 4.6 2.3 + - - -
430A GLU* 3.1 21.4 + - + +
431A GLY* 3.6 14.7 - - - +
432A ILE* 3.9 26.5 - - + +
439A ILE* 1.3 81.4 - - - +
441A SER* 1.3 77.3 + - - +
442A PHE* 2.7 19.1 + - - +
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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