Contacts of the strand formed by residues 514 - 521 (chain A) in PDB entry 4X7C
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 TYR 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A ILE* 3.7 38.6 - - + +
232A LEU 3.6 20.4 - - - +
233A THR* 4.6 1.3 - - + +
476A ARG 3.6 0.2 - - - +
477A PHE* 3.4 10.8 - - - -
478A VAL* 2.8 61.4 + - + +
480A PRO* 3.8 23.9 - - + +
512A ASN 3.8 13.2 - - - +
513A GLY* 1.3 74.1 - - - +
515A PHE* 1.3 82.1 + - - +
516A ARG* 4.1 18.2 + - + -
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Residues in contact with PHE 515 (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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229A VAL* 3.5 17.2 - - + +
230A PRO 3.6 9.3 + - - +
231A ILE* 4.6 1.4 - - - +
232A LEU 4.8 2.1 + - - -
234A VAL* 4.6 5.4 - - + -
237A MET* 5.2 6.3 - - + -
249A LEU* 3.8 20.2 - - + -
432A LEU* 4.2 8.1 - - + -
434A PHE* 3.8 28.3 - + - -
457A TRP* 3.6 31.6 - + + -
475A LEU* 4.0 20.9 - - + -
476A ARG 3.5 2.5 - - - -
477A PHE* 3.4 37.0 - + + -
487A PHE* 4.2 8.3 - + - -
489A CYS* 3.8 22.9 - - - -
497A VAL* 5.4 0.7 - - + -
514A TYR* 1.3 86.4 - - - +
516A ARG* 1.3 60.5 + - - +
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Residues in contact with ARG 516 (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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229A VAL* 4.4 1.3 - - - -
231A ILE* 6.3 0.4 - - + -
475A LEU* 3.3 4.9 - - - -
476A ARG* 2.8 38.7 + - - +
478A VAL* 3.7 24.3 - - + +
483A GLY 5.0 7.3 + - - -
485A VAL* 3.9 21.4 - - - +
514A TYR* 4.1 22.4 + - + -
515A PHE* 1.3 76.2 - - - +
517A PHE* 1.3 68.5 + - - +
518A ASP* 2.7 38.6 + - - +
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Residues in contact with PHE 517 (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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227A PHE* 3.3 34.5 - + + -
228A THR* 4.4 2.0 - - - -
229A VAL* 4.2 22.8 - - - +
473A ALA* 3.3 31.2 - - + -
474A LEU 3.7 6.7 - - - -
475A LEU* 3.8 13.0 - - + -
516A ARG* 1.3 77.3 - - - +
518A ASP* 1.3 62.1 + - - +
519A SER* 3.3 34.5 - - - -
520A TRP* 3.5 27.4 - + - -
102C ALA* 3.5 35.0 - - + +
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Residues in contact with ASP 518 (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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474A LEU* 2.9 16.4 + - + +
476A ARG* 2.8 39.7 + - - +
516A ARG* 2.7 44.4 + - - +
517A PHE* 1.3 79.5 - - - +
519A SER* 1.3 68.5 + - - +
31C ILE* 3.7 20.2 - - + +
102C ALA* 3.7 14.8 + - - +
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Residues in contact with SER 519 (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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474A LEU* 2.7 39.7 + - - +
517A PHE* 3.3 12.2 - - - -
518A ASP* 1.3 84.1 + - - +
520A TRP* 1.3 58.9 + - - +
521A VAL* 4.3 2.7 - - - -
31C ILE* 3.5 22.4 - - - +
100C TYR* 3.6 20.9 + - - -
101C SER* 3.3 28.4 + - - -
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Residues in contact with TRP 520 (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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227A PHE* 3.5 39.8 - + + +
268A THR* 4.2 12.8 - - - -
466A ALA 5.5 0.2 - - - -
467A PRO 4.0 3.6 + - - -
468A ALA* 3.5 21.1 - - + -
469A GLN* 3.5 38.7 - - + +
470A SER* 3.3 42.8 - - - +
472A VAL 3.6 11.9 - - - -
473A ALA* 3.9 18.4 - - + -
491A LEU 5.5 0.2 - - - -
493A LYS* 5.1 2.9 - - + -
517A PHE* 3.5 22.7 - + - -
519A SER* 1.3 69.4 - - - +
521A VAL* 1.3 60.6 + - - +
100C TYR* 3.2 22.3 - - - +
101C SER 2.9 16.3 + - - +
102C ALA 3.7 18.1 + - - -
104C ALA 3.9 11.7 - - - +
106C PRO* 3.7 7.9 - - + +
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Residues in contact with VAL 521 (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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470A SER* 2.6 30.8 + - - -
472A VAL* 2.9 40.4 + - + +
474A LEU* 3.8 31.6 - - + -
490A LYS* 4.2 6.7 - - - -
519A SER* 3.5 2.9 + - - +
520A TRP* 1.3 76.5 - - - +
522A ASN* 1.3 69.6 + - - +
525A TYR* 3.8 25.4 - - + -
31C ILE* 4.5 0.2 - - + -
100C TYR* 3.5 30.7 - - + -
106C PRO* 4.1 1.8 - - - -
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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