Contacts of the strand formed by residues 335 - 340 (chain A) in PDB entry 5E0F
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 PHE 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PRO* 3.6 40.2 - - + -
6A THR* 4.3 6.5 - - + -
10A ARG 4.9 0.7 - - - -
11A THR* 3.3 37.2 - - - -
12A SER 4.1 1.6 - - - -
13A ILE* 3.7 33.9 - - + -
229A PHE* 4.3 10.8 - + - -
252A ARG* 3.7 23.7 - - - +
292A ALA 3.0 10.4 + - - +
293A LEU* 3.4 25.2 - - + +
294A VAL* 2.9 23.8 + - - -
334A GLY* 1.3 71.2 - - - -
336A THR* 1.3 68.9 + - - +
398A ARG* 5.0 0.7 - - - +
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Residues in contact with THR 336 (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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11A THR 3.3 3.4 + - - -
12A SER* 2.8 27.8 + - - -
13A ILE* 3.0 24.8 + - - +
294A VAL* 3.7 11.9 - - + -
328A MET* 3.7 35.2 - - + +
329A LEU* 3.8 11.7 - - + -
333A TYR 4.8 0.2 - - - +
334A GLY 4.0 0.4 + - - -
335A PHE* 1.3 78.7 - - - +
337A ARG* 1.3 60.1 + - - +
338A VAL 4.2 0.2 - - - -
398A ARG* 3.1 38.3 + - - +
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Residues in contact with ARG 337 (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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13A ILE* 3.2 28.3 - - + +
15A HIS* 4.3 16.3 - - + +
41A GLN* 2.9 36.9 + - - +
195A ARG* 4.4 0.4 - - - +
231A TYR* 3.8 13.5 - - - -
254A THR* 4.9 0.2 - - - +
293A LEU* 3.9 18.0 - - + +
294A VAL 2.9 14.3 + - - +
295A PHE* 3.4 52.4 - - - +
296A VAL 4.7 0.7 + - - -
297A ASP 5.2 2.0 + - - -
298A ASN* 3.5 16.6 - - - +
299A HIS* 6.4 0.2 - - - -
328A MET* 3.8 6.9 - - - +
336A THR* 1.3 73.4 - - - +
338A VAL* 1.3 73.3 + - - +
339A MET* 4.1 1.9 + - - +
503A CL 3.1 32.7 - - - +
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Residues in contact with VAL 338 (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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12A SER* 5.0 4.0 - - - +
13A ILE 2.8 11.3 + - - +
14A VAL* 3.2 6.9 - - + -
15A HIS 2.8 25.8 + - - -
37A PHE* 5.2 2.2 - - + -
321A TYR* 5.7 1.6 - - + +
325A VAL* 4.7 4.9 - - + -
328A MET* 4.6 6.5 - - + -
329A LEU* 4.3 22.2 - - + -
337A ARG* 1.3 78.6 - - - +
339A MET* 1.3 74.0 + - - +
385A GLU* 5.1 1.6 - - + -
386A HIS* 4.2 16.8 - - + +
391A ILE* 4.0 22.2 - - + -
395A VAL* 4.2 23.8 - - + -
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Residues in contact with MET 339 (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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15A HIS* 3.7 21.5 - - - -
17A PHE* 3.8 22.4 - - + -
297A ASP* 3.5 31.6 + - - +
298A ASN* 4.2 4.3 - - - -
299A HIS* 3.9 19.3 - - + -
302A GLN* 3.7 26.0 - - - +
321A TYR* 3.5 9.5 + - - +
337A ARG* 4.1 3.2 + - - +
338A VAL* 1.3 86.9 - - - +
340A SER* 1.3 77.8 + - - +
341A SER* 3.4 24.7 - - - +
385A GLU* 3.5 18.5 - - - +
386A HIS 4.3 0.2 + - - -
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Residues in contact with SER 340 (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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14A VAL* 3.9 3.8 - - - -
15A HIS 3.0 24.2 + - - +
16A LEU* 3.7 13.9 - - - +
17A PHE* 3.4 21.8 + - - +
19A TRP* 4.4 7.5 + - - -
339A MET* 1.3 77.1 - - - +
341A SER* 1.3 61.5 + - - +
384A CYS* 3.5 12.8 + - - -
385A GLU* 3.3 4.3 - - - -
386A HIS* 2.8 36.3 + - - -
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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