Contacts of the strand formed by residues 275 - 279 (chain 7) in PDB entry 3J7Y
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 CYS 275 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1427 TYR* 3.6 34.1 - - - +
1457 SER* 5.0 7.4 - - - -
1467 CYS* 4.3 8.3 - - - -
1497 MET* 3.4 26.9 - - + -
2107 ILE* 3.3 34.5 - - + +
2697 ILE* 6.1 0.9 - - - -
2717 ARG 5.3 1.6 - - - -
2727 THR* 3.2 14.9 + - - +
2737 SER 3.0 12.5 - - - +
2747 ILE* 1.3 75.4 - - - +
2767 PHE* 1.3 58.0 + - - +
2787 TYR* 4.4 6.7 - - + -
3027 LEU 5.4 0.2 - - - +
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Residues in contact with PHE 276 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2077 HIS* 3.8 16.5 + - - -
2107 ILE* 5.0 2.3 - - - +
2747 ILE 3.4 1.6 + - - -
2757 CYS* 1.3 74.0 - - - +
2777 GLN* 1.3 89.6 + - + +
2787 TYR* 3.7 3.3 + - - +
3027 LEU 3.4 4.9 + - - -
3037 PRO 3.6 3.1 - - - -
3047 VAL* 3.5 33.2 - - + +
3077 ARG* 3.6 56.1 - - + -
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Residues in contact with GLN 277 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427 TYR* 4.7 0.2 + - - -
2077 HIS* 4.8 2.0 - - - -
2767 PHE* 1.3 103.2 + - + +
2787 TYR* 1.3 58.3 + - - +
3017 SER* 3.1 5.7 - - - -
3027 LEU* 2.8 48.9 + - - +
3077 ARG* 4.9 1.0 - - - +
3087 ALA* 3.1 34.1 + - - +
3097 HIS* 3.9 19.2 - - - +
3107 PHE 5.5 0.2 - - - +
3137 TRP* 3.5 42.2 - - + +
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Residues in contact with TYR 278 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467 CYS* 2.6 31.6 + - + -
1497 MET* 3.3 28.0 - - + -
1507 MET* 3.1 17.5 + - + +
1797 PHE* 3.2 28.3 - + - -
2037 THR* 4.6 1.9 - - - -
2067 ALA* 3.3 33.9 - - + -
2077 HIS* 3.0 30.1 + - + -
2107 ILE* 3.6 22.7 - - + -
2757 CYS* 4.4 7.4 - - + -
2767 PHE 3.7 2.8 + - - -
2777 GLN* 1.3 74.4 - - - +
2797 GLU* 1.3 68.6 + - - +
2807 VAL* 4.5 14.1 - - + -
3007 VAL 4.3 0.2 - - - -
3017 SER* 3.3 22.7 - - - -
3137 TRP* 4.2 0.8 - - - -
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Residues in contact with GLU 279 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1797 PHE* 4.2 5.9 - - - -
2037 THR* 4.0 14.4 - - + +
2077 HIS* 5.0 3.6 - - - +
2787 TYR* 1.3 82.8 - - - +
2807 VAL* 1.3 67.9 + - - +
2817 SER 4.0 0.7 - - - -
2997 GLY* 3.5 3.8 - - - -
3007 VAL 3.2 29.7 + - - +
3137 TRP* 2.8 32.4 + - + +
3177 LEU* 3.2 42.1 - - + +
3217 ARG* 5.4 3.8 + - - -
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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