Contacts of the strand formed by residues 335 - 342 (chain A) in PDB entry 4NEN
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 GLU 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY 5.1 0.2 - - - -
91A PRO* 4.2 2.1 - - - +
104A THR* 2.2 31.2 + - - -
105A GLY* 3.0 30.8 + - - +
106A LEU 4.1 0.9 + - - -
107A CYS* 4.8 0.9 - - - -
120A PRO* 4.6 15.9 - - + +
124A GLN* 5.8 0.3 + - - -
330A LEU* 4.1 8.3 - - - +
333A ALA* 3.3 19.5 - - + +
334A GLN* 1.3 73.2 - - - +
336A GLY* 1.3 61.3 + - - +
348A LEU* 4.6 5.8 - - + -
350A ALA* 3.8 12.8 - - + -
361A PHE* 3.9 31.3 - - + -
363A TYR* 4.5 14.1 - - - +
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Residues in contact with GLY 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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76A SER* 2.9 21.1 + - - -
89A CYS* 3.3 9.5 - - - +
91A PRO* 3.7 8.0 - - - +
107A CYS* 3.9 16.2 - - - -
335A GLU* 1.3 74.9 - - - +
337A PHE* 1.3 62.0 + - - +
338A SER 3.2 6.7 - - - -
348A LEU* 3.7 22.8 - - - +
349A GLY 3.1 8.1 + - - -
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Residues in contact with PHE 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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75A LEU* 4.7 16.4 - - + +
76A SER* 3.3 16.0 - - - -
91A PRO* 3.7 23.0 - - + +
334A GLN* 3.4 32.3 + - - +
336A GLY* 1.3 78.9 - - - +
338A SER* 1.3 58.5 + - - +
349A GLY 3.0 7.8 + - - +
351A VAL* 3.5 27.4 - - + -
387A GLY 4.7 0.2 - - - +
388A TYR* 3.4 61.1 - + - +
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Residues in contact with SER 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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76A SER* 4.3 5.8 - - - -
336A GLY 3.9 4.3 - - - -
337A PHE* 1.3 77.3 - - - +
339A ALA* 1.3 62.7 + - - +
348A LEU* 3.5 2.8 - - - -
349A GLY* 2.7 26.2 + - - -
387A GLY 2.9 13.0 + - - -
388A TYR 3.5 20.2 - - - -
389A SER* 3.9 0.9 - - - -
390A THR* 2.3 40.2 + - - -
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Residues in contact with ALA 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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76A SER* 4.8 4.8 + - - +
77A LEU 4.6 5.1 + - - +
78A ALA* 3.5 20.9 - - + +
87A LEU* 3.7 15.9 - - + +
89A CYS* 4.2 11.4 - - - -
338A SER* 1.3 78.4 + - - +
340A VAL* 1.3 65.2 + - - +
347A VAL 3.3 4.7 - - - -
348A LEU* 3.7 22.2 - - + -
390A THR* 4.4 7.8 - - - +
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Residues in contact with VAL 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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78A ALA* 4.4 5.2 - - - -
87A LEU* 5.2 1.5 - - - +
339A ALA* 1.3 77.3 - - - +
341A PHE* 1.3 71.4 + - - +
342A THR* 4.2 12.3 - - + -
346A PRO* 3.8 1.7 - - - +
347A VAL* 2.9 39.8 + - + +
390A THR* 3.6 31.2 - - + +
391A GLU* 3.8 22.4 - - - +
392A LEU* 4.0 20.0 - - + +
401A LEU* 4.3 2.0 - - + -
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Residues in contact with PHE 341 (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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78A ALA* 3.6 15.0 - - + -
79A SER* 3.8 27.4 - - - +
80A THR* 3.6 26.5 - - + +
85A GLN* 3.7 32.1 - - + -
87A LEU* 3.5 30.5 - - + -
109A LEU* 3.6 30.3 - - + -
340A VAL* 1.3 80.6 - - - +
342A THR* 1.3 65.3 - - - +
345A GLY 4.5 1.1 - - - -
346A PRO* 4.4 20.9 - - + -
392A LEU* 3.4 19.8 - - - +
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Residues in contact with THR 342 (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 VAL* 4.2 10.1 - - + -
341A PHE* 1.3 82.8 - - - +
343A PRO* 1.3 75.4 - - - +
344A ASP* 3.7 3.6 + - - -
345A GLY* 2.2 48.3 + - - +
347A VAL* 3.7 22.2 - - + -
362A LEU* 3.8 9.5 - - - +
392A LEU* 3.7 20.0 - - + -
399A GLN* 4.3 8.3 + - - +
401A LEU* 4.4 6.3 - - + -
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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