Contacts of the strand formed by residues 349 - 356 (chain A) in PDB entry 3REO
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 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A ALA* 5.0 1.4 - - - +
347A PHE* 3.7 4.7 - - - +
348A ARG* 1.3 76.5 - - - +
350A PHE* 1.3 61.9 + - - +
364A PHE* 3.6 4.2 - - - -
365A LEU* 2.8 47.2 + - - +
367A THR 5.0 3.8 - - - -
9D ILE 5.5 0.7 - - - -
10D GLN* 3.3 13.0 - - - -
12D ILE* 4.9 2.7 - - - -
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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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335A GLU* 3.5 26.7 - - + -
338A PHE* 3.9 2.5 - - + -
339A GLN* 3.5 52.9 - - + -
342A ALA* 4.2 5.2 - - + -
349A GLY* 1.3 75.0 - - - +
351A LYS* 1.3 65.3 + - - +
352A VAL* 3.8 13.5 - - + -
362A MET* 3.6 26.2 - - + -
363A GLU 3.4 5.6 - - - -
364A PHE* 3.4 37.9 - + - -
365A LEU* 5.5 0.2 - - - -
9D ILE 5.4 6.3 - - - +
10D GLN 2.9 9.9 + - - +
11D ILE* 3.4 13.5 - - + +
12D ILE* 2.8 28.7 + - - +
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Residues in contact with LYS 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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198A TYR* 6.2 0.2 - - - -
350A PHE* 1.3 81.3 - - - +
352A VAL* 1.3 65.2 + - - +
353A ALA* 4.3 14.5 - - + +
362A MET* 3.2 6.9 - - - +
363A GLU* 2.9 69.3 + - + +
365A LEU* 5.2 0.4 - - + -
11D ILE* 5.5 1.1 - - - -
12D ILE* 3.7 40.8 - - + +
13D PRO 5.2 0.4 + - - -
14D THR* 3.5 21.8 - - + -
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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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302A ILE* 5.2 2.7 - - + -
335A GLU* 3.6 36.3 - - + +
350A PHE* 3.8 10.3 - - + -
351A LYS* 1.3 72.8 - - - +
353A ALA* 1.3 62.7 + - - +
354A SER* 4.4 4.3 - - - +
360A TYR* 3.9 28.9 - - + -
361A VAL 3.8 7.2 - - - +
362A MET* 4.1 11.4 - - + -
12D ILE 5.1 0.2 + - - -
14D THR* 3.2 27.9 + - - +
16D SER* 3.8 28.9 + - - +
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Residues in contact with ALA 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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198A TYR* 3.4 35.0 - - + -
351A LYS* 3.8 25.9 + - + +
352A VAL* 1.3 74.1 - - - +
354A SER* 1.3 64.0 + - - +
361A VAL 2.8 16.9 + - - +
363A GLU* 4.6 3.8 - - + -
14D THR* 4.8 3.0 - - - -
15D HIS* 6.1 2.8 - - - +
16D SER* 6.1 0.4 - - - -
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Residues in contact with SER 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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194A ILE* 5.0 1.2 - - - +
197A MET* 4.2 26.9 - - - +
198A TYR* 3.6 28.6 - - - +
352A VAL* 3.8 3.6 - - - +
353A ALA* 1.3 81.0 - - - +
355A CYS* 1.3 62.4 + - - +
360A TYR* 3.4 8.7 - - - -
361A VAL* 2.8 35.2 + - - +
16D SER* 6.5 0.2 - - - -
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Residues in contact with CYS 355 (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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193A LYS* 4.5 4.0 + - - -
194A ILE* 5.0 0.9 - - - -
197A MET* 3.2 19.9 - - - +
354A SER* 1.3 82.6 + - - +
356A ALA* 1.3 63.1 + - - +
357A PHE 5.0 0.2 - - - -
358A ASN* 4.1 13.7 - - - -
359A THR 3.1 15.9 - - - -
360A TYR* 3.5 42.8 - - + -
361A VAL* 5.1 0.8 - - - +
19C GLU* 5.1 0.8 - - - +
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Residues in contact with ALA 356 (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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190A THR* 3.8 6.7 - - + +
193A LYS* 3.4 39.5 - - + +
194A ILE* 3.7 20.8 - - + +
197A MET* 4.1 0.7 - - + -
355A CYS* 1.3 73.4 - - - +
357A PHE* 1.4 75.6 + - + +
358A ASN 3.2 2.0 - - - -
359A THR* 2.8 23.9 + - - -
19C GLU* 3.9 5.2 - - - -
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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