Contacts of the strand formed by residues 503 - 510 (chain A) in PDB entry 3FCS
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 SER 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A LYS 4.4 0.2 - - - -
502A LEU* 1.3 85.8 - - - +
504A LEU* 1.3 77.5 + - - +
505A ASN* 5.2 0.7 + - - -
534A ASN* 4.5 7.8 - - - +
535A LEU 3.0 19.5 + - - -
536A ASP* 4.4 4.8 - - - -
573A LEU* 3.8 0.3 - - - +
574A PRO* 3.2 29.6 - - - +
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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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454A VAL* 5.4 0.9 - - + -
456A ALA* 4.8 4.0 - - + -
491A VAL* 4.5 7.0 - - + -
493A ALA* 4.6 8.1 - - + -
502A LEU* 4.3 6.0 - - + +
503A SER* 1.3 84.3 + - - +
505A ASN* 1.3 65.7 + - - +
506A ALA* 6.3 0.2 - - + -
533A LEU 3.7 0.3 - - - +
534A ASN* 3.7 1.6 - - - -
535A LEU* 2.9 35.4 + - + +
537A LEU* 3.5 30.5 - - + -
571A VAL* 3.5 24.9 - - + -
572A SER 3.3 20.4 - - - +
573A LEU* 3.4 25.1 - - + -
574A PRO* 4.3 1.8 - - - -
586A LEU* 4.0 20.2 - - + -
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Residues in contact with ASN 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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503A SER* 5.2 0.5 + - - -
504A LEU* 1.3 75.7 - - - +
506A ALA* 1.3 60.4 + - - +
532A THR* 4.0 9.4 - - + -
533A LEU 3.2 2.7 - - - -
534A ASN* 2.8 29.2 + - - +
571A VAL* 3.3 6.6 - - - +
572A SER* 2.9 38.5 + - - +
573A LEU 4.6 0.4 + - - -
574A PRO* 3.8 33.7 - - - +
575A PRO* 4.8 4.4 - - - +
3570A NAG 3.5 18.6 - - + +
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Residues in contact with ALA 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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489A MET* 5.3 2.4 - - - +
491A VAL* 4.5 1.6 - - + -
504A LEU 3.9 0.2 + - - -
505A ASN* 1.3 72.7 - - - +
507A GLU* 1.3 62.7 + - - +
508A LEU* 3.8 2.8 + - - +
531A THR 3.8 0.5 - - - +
532A THR* 3.4 2.4 - - - -
533A LEU* 2.7 46.5 + - + +
535A LEU* 3.9 27.6 - - + -
569A LEU* 4.1 16.9 - - + +
570A ASN 3.5 5.2 - - - -
571A VAL* 4.4 9.9 - - + -
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Residues in contact with GLU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ALA* 1.3 71.2 - - - +
508A LEU* 1.3 61.0 + - - +
509A GLN* 3.1 36.4 + - + +
512A ARG* 5.5 1.2 + - - -
531A THR 3.5 6.1 - - - +
532A THR* 3.9 18.3 + - - +
568A SER* 3.6 2.1 + - - +
569A LEU* 3.3 7.8 - - - +
570A ASN* 2.8 42.0 + - + +
3570A NAG 3.3 52.4 + - + +
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Residues in contact with LEU 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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460A LEU* 4.2 25.4 - - + -
487A ILE* 4.6 11.0 - - + -
489A MET* 3.8 37.2 - - + -
506A ALA 3.8 1.0 + - - +
507A GLU* 1.3 72.2 - - - +
509A GLN* 1.3 67.3 + - - +
510A LEU* 3.8 21.5 - - + -
523A LEU* 4.5 4.9 - - + -
530A GLY* 3.0 24.8 - - - -
531A THR* 2.8 23.0 + - - +
533A LEU* 6.5 0.2 - - + -
548A THR* 4.0 20.6 - - + -
567A LEU* 5.0 3.8 - - + -
568A SER 3.4 16.2 - - - +
569A LEU* 4.5 1.8 - - + -
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Residues in contact with GLN 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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507A GLU* 3.1 34.1 + - + +
508A LEU* 1.3 83.5 + - - +
510A LEU* 1.3 64.2 + - - +
512A ARG* 4.2 24.2 + - + +
519A ARG* 3.5 18.9 + - - +
529A ALA* 3.3 15.2 - - - +
530A GLY* 3.8 10.7 + - - -
531A THR 4.6 0.4 - - - +
566A VAL 3.8 1.2 - - - +
567A LEU* 3.5 6.9 - - - +
568A SER* 3.0 46.8 + - - +
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Residues in contact with LEU 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A ILE* 4.2 4.9 - - + -
508A LEU* 3.8 30.5 - - + +
509A GLN* 1.3 75.3 - - - +
511A ASP* 1.3 72.1 + - - +
519A ARG* 2.9 19.6 + - - +
521A VAL* 3.7 18.8 - - + +
522A LEU* 3.7 25.1 - - - +
523A LEU* 4.0 14.4 - - + +
529A ALA* 2.8 26.6 + - - +
530A GLY* 4.6 0.4 - - - -
550A ALA* 3.5 31.6 - - + -
567A LEU* 3.7 15.7 - - + -
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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