Contacts of the strand formed by residues 502 - 510 (chain A) in PDB entry 3FL7
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 THR 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A LYS* 3.9 1.4 - - - +
476A LYS* 3.0 41.9 + - + +
501A THR* 1.3 82.6 - - - +
503A TYR* 1.3 62.5 + - - +
523A GLU* 3.6 41.5 - - + +
524A PHE 3.9 4.3 - - - +
525A GLN* 4.8 5.9 - - + +
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Residues in contact with TYR 503 (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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452A LEU* 3.6 25.1 - - + -
473A TYR* 5.1 11.7 - + + -
474A ARG 3.2 23.1 - - - +
475A LYS* 3.9 24.4 - - + +
497A LEU* 3.4 38.0 - - + +
498A ALA* 3.0 29.4 + - - +
501A THR* 3.9 22.8 - - + +
502A THR* 1.3 75.7 - - - +
504A LEU* 1.3 62.1 + - - +
505A VAL* 3.7 10.5 + - + +
522A HIS 3.1 13.5 - - - +
523A GLU* 3.3 4.3 - - - +
524A PHE 3.2 22.7 + - - +
526A THR* 4.1 9.4 - - + -
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Residues in contact with LEU 504 (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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472A THR* 3.4 2.3 - - - +
473A TYR* 3.3 6.5 - - - -
474A ARG* 3.0 57.8 + - + +
476A LYS* 4.5 23.8 - - + -
503A TYR* 1.3 71.2 - - - +
505A VAL* 1.3 61.2 + - - +
506A GLN 4.1 0.3 + - - -
521A VAL* 3.8 22.4 - - + -
522A HIS 3.5 2.5 - - - -
523A GLU* 3.8 31.6 - - + +
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Residues in contact with VAL 505 (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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442A VAL* 5.3 2.9 - - + +
452A LEU* 5.0 2.5 - - + -
454A VAL* 4.9 7.2 - - + -
471A VAL* 4.5 12.8 - - + -
472A THR 3.3 7.6 - - - +
473A TYR* 4.3 13.0 - - + -
494A LEU* 4.6 15.5 - - + -
503A TYR* 4.4 14.4 - - + +
504A LEU* 1.3 76.4 - - - +
506A GLN* 1.3 68.8 + - - +
507A VAL* 4.6 9.0 - - + -
520A LYS 3.7 2.4 - - - +
521A VAL* 3.6 3.3 - - - -
522A HIS* 2.9 38.6 + - - +
524A PHE* 3.9 36.8 - - + -
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Residues in contact with GLN 506 (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 GLU 3.5 0.9 - - - +
471A VAL* 3.5 4.2 - - - +
472A THR* 2.9 41.5 + - - +
504A LEU 4.1 0.8 + - - -
505A VAL* 1.3 73.8 - - - +
507A VAL* 1.3 71.9 + - - +
508A GLN* 4.1 6.1 - - + +
518A GLY* 4.0 13.3 + - - -
519A SER* 2.9 34.5 + - - +
520A LYS 4.5 1.3 - - - +
521A VAL* 3.4 25.1 - - + +
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Residues in contact with VAL 507 (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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440A PRO* 3.2 33.2 - - + +
442A VAL* 4.3 20.0 - - + -
454A VAL* 5.1 1.1 - - + -
456A TRP* 4.1 35.7 - - + -
469A TYR* 4.2 8.5 - - + -
470A GLU 3.5 5.4 - - - +
471A VAL* 4.0 17.9 - - + -
505A VAL* 4.6 8.3 - - + -
506A GLN* 1.3 79.9 - - - +
508A GLN* 1.3 64.1 + - - +
519A SER* 3.0 32.9 + - - +
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Residues in contact with GLN 508 (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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440A PRO* 4.5 1.8 - - - -
469A TYR* 3.3 7.8 - - - +
470A GLU* 2.8 51.2 + - + +
506A GLN* 4.1 7.4 - - + +
507A VAL* 1.3 73.5 - - - +
509A ALA* 1.3 64.4 + - - +
510A LEU* 3.6 24.4 + - + +
516A GLY 3.7 24.7 + - - +
517A ALA 3.9 4.0 - - - +
518A GLY* 3.7 21.7 - - - +
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Residues in contact with ALA 509 (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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437A THR* 6.5 0.2 - - + -
438A GLU 5.0 7.2 - - - +
440A PRO* 4.2 9.1 - - + +
458A ILE* 5.5 2.0 - - + -
466A VAL* 3.6 24.5 - - + -
469A TYR* 4.0 16.8 - - + -
507A VAL 4.0 1.0 + - - -
508A GLN* 1.3 71.3 - - - +
510A LEU* 1.3 61.8 + - - +
511A THR* 5.1 1.9 - - - +
516A GLY* 3.4 7.4 + - - -
517A ALA* 2.8 40.7 + - + +
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Residues in contact with LEU 510 (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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466A VAL* 3.4 5.3 - - - +
467A TRP* 2.6 34.5 + - + -
468A LYS* 2.9 26.4 + - + +
470A GLU* 3.8 21.5 - - + +
486A ARG* 3.5 37.9 - - - +
508A GLN* 3.6 43.3 - - + +
509A ALA* 1.3 74.5 - - - +
511A THR* 1.3 57.9 + - - +
516A GLY 4.4 6.1 - - - +
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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