Contacts of the strand formed by residues 388 - 391 (chain A) in PDB entry 3E4E
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 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 3.6 29.6 - - + -
76A ARG 3.1 11.7 + - - +
77A MET* 3.5 17.8 - - + -
78A VAL 3.0 24.6 + - - -
101A GLY* 4.5 14.4 - - - -
102A ASP 5.0 4.9 - - - +
369A PRO* 3.9 20.6 - - + -
370A HIS 3.4 11.0 - - - +
371A GLU* 4.0 4.9 - - + +
386A GLY 3.4 3.0 + - - +
387A THR* 1.3 76.6 - - - +
389A VAL* 1.3 62.4 + - - +
390A VAL* 4.2 14.1 - - + -
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Residues in contact with VAL 389 (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 VAL* 3.5 9.6 - - + -
80A MET* 4.2 19.7 - - + -
89A ALA* 5.2 0.7 - - + -
97A PHE* 4.0 44.2 - - + -
370A HIS* 2.6 46.4 + - + +
371A GLU* 4.4 1.1 - - - -
372A ALA 4.3 1.8 - - - +
383A ILE* 4.1 15.3 - - + -
387A THR* 3.8 10.5 - - + +
388A VAL* 1.3 79.6 - - - +
390A VAL* 1.3 64.1 + - - +
391A PRO* 3.3 18.0 - - + +
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Residues in contact with VAL 390 (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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57A PHE* 4.1 22.0 - - + -
77A MET* 4.0 30.5 - - + -
78A VAL 2.8 13.7 + - - +
79A VAL* 3.7 8.5 - - + -
80A MET* 3.0 24.7 + - - +
366A SER* 3.4 29.2 - - - +
369A PRO* 4.9 9.0 - - + -
388A VAL* 4.2 9.9 - - + -
389A VAL* 1.3 78.4 - - - +
391A PRO* 1.3 61.4 - - + +
392A THR* 3.1 13.9 + - - +
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Residues in contact with PRO 391 (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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80A MET* 4.0 7.4 - - + +
86A VAL* 4.0 13.9 - - + +
89A ALA* 4.8 7.4 - - + -
90A LEU* 3.5 43.1 - - + -
97A PHE* 6.2 0.4 - - + -
367A ASN* 3.1 35.4 + - + +
368A LEU 4.5 1.6 - - - +
370A HIS* 4.1 16.8 - - + -
389A VAL* 3.3 24.2 - - + +
390A VAL* 1.3 79.7 - - - +
392A THR* 1.3 65.9 + - - +
393A LEU* 3.4 2.3 + - - +
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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