Contacts of the strand formed by residues 578 - 586 (chain A) in PDB entry 3F8I
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 LEU 578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A SER 4.3 1.4 - - - +
503A ASP* 2.8 31.4 + - + +
504A GLN* 3.0 36.7 + - - +
570A PRO* 4.3 17.7 - - + -
571A GLU* 3.8 22.9 - - - +
572A ARG* 4.3 15.1 - - + +
576A GLY 4.2 0.6 + - - -
577A PHE* 1.3 73.7 - - - +
579A VAL* 1.3 66.6 + - - +
580A TRP* 5.1 6.7 - - + +
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Residues in contact with VAL 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ASP* 3.6 28.3 - - - +
484A THR* 4.1 9.2 - - + -
500A GLN* 4.3 17.3 - - + +
504A GLN* 3.4 21.1 - - + +
570A PRO* 3.5 3.6 - - - +
571A GLU* 3.0 39.2 + - + +
572A ARG 4.5 0.2 - - - -
573A GLY* 3.9 11.2 - - - -
575A SER* 5.2 0.9 - - - +
577A PHE* 3.8 8.3 - - + +
578A LEU* 1.3 81.3 - - - +
580A TRP* 1.3 64.4 + - - +
581A ARG* 3.8 18.3 + - + +
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Residues in contact with TRP 580 (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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484A THR* 3.3 6.9 - - - +
485A GLY 2.8 28.0 + - - +
504A GLN* 2.8 34.0 + - + +
505A LYS* 3.6 20.9 - - - +
506A LEU* 3.5 42.6 - - + +
510A ASN* 4.3 3.8 - - - +
523A GLU* 3.1 32.1 - - + -
525A GLY 4.2 3.1 - - - -
568A TYR* 4.1 18.6 - + + -
569A TRP* 3.6 23.8 - - - -
570A PRO* 3.3 38.2 - - + +
578A LEU* 5.1 5.6 - - + +
579A VAL* 1.3 73.0 - - - +
581A ARG* 1.3 59.2 + - - +
582A TYR* 3.7 21.0 - - + +
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Residues in contact with ARG 581 (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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473A ASP* 2.9 37.9 + - - +
475A VAL* 3.6 18.2 - - - +
482A THR* 3.8 16.1 - - + +
483A TYR 3.4 6.5 + - - +
484A THR* 5.3 3.7 + - + -
568A TYR* 3.0 5.9 - - - +
569A TRP* 2.8 65.5 + - + +
571A GLU* 3.1 40.4 + - + -
579A VAL* 4.1 18.4 - - + +
580A TRP* 1.3 78.5 - - - +
582A TYR* 1.3 64.2 + - - +
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Residues in contact with TYR 582 (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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482A THR* 3.3 7.9 - - - +
483A TYR* 2.9 44.6 + - + +
484A THR 4.5 0.7 - - - -
485A GLY* 4.0 13.0 - - - -
506A LEU* 4.1 4.8 - - + +
510A ASN* 2.8 35.6 + - - +
513A LEU* 3.6 32.1 - - + -
514A ALA* 3.7 24.7 - - + -
565A VAL* 4.4 9.4 - - + -
567A LYS 3.5 4.7 - - - +
568A TYR* 3.5 21.8 - + + -
569A TRP* 4.5 0.9 - - - -
580A TRP* 3.7 31.4 - + + +
581A ARG* 1.3 73.8 - - - +
583A LEU* 1.3 60.6 - - - +
584A LEU* 3.5 20.5 - - + +
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Residues in contact with LEU 583 (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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480A TYR* 4.5 25.4 - - + -
481A PHE 3.7 15.0 - - - +
482A THR* 4.0 12.8 - - - +
565A VAL* 3.5 4.3 - - - -
566A VAL* 2.8 45.5 + - + -
567A LYS* 2.8 46.5 + - + +
569A TRP* 4.2 8.5 - - + -
582A TYR* 1.3 73.3 - - - +
584A LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 584 (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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465A LEU* 4.0 18.2 - - + -
480A TYR* 3.3 7.1 - - - +
481A PHE* 3.0 74.7 + - + +
483A TYR* 4.0 6.1 - - + -
513A LEU* 4.8 2.0 - - + -
537A VAL* 4.8 9.9 - - + -
563A TYR* 4.2 16.4 - - + -
564A LYS 3.1 10.5 - - - +
565A VAL* 4.1 19.1 - - + -
582A TYR* 3.5 32.8 - - + +
583A LEU* 1.3 79.1 - - - +
585A ARG* 1.3 61.6 + - - +
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Residues in contact with ARG 585 (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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479A ASN* 3.3 9.0 - - + +
480A TYR* 3.1 43.6 + - + -
531A TRP* 3.3 52.9 - - + +
563A TYR* 3.2 5.1 - - - -
564A LYS* 2.8 30.3 + - - -
566A VAL* 3.8 19.0 - - + +
583A LEU 4.3 0.2 - - - -
584A LEU* 1.3 74.8 - - - +
586A ARG* 1.3 72.7 + - - +
587A ASP 3.6 0.2 + - - -
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Residues in contact with ARG 586 (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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431A VAL* 3.8 10.5 - - - +
479A ASN* 2.9 34.7 + - + +
531A TRP* 3.8 5.7 - - - -
560A ASP 2.8 28.1 + - - -
562A ILE 3.5 9.9 - - - +
563A TYR* 3.2 35.5 + - + -
585A ARG* 1.3 84.8 + - - +
587A ASP* 1.3 62.6 + - - +
588A ASP* 3.7 27.2 + - - +
590A GLU 2.8 32.3 + - - -
591A PRO* 3.8 9.5 + - - +
592A GLU* 3.8 27.4 + - - +
594A TRP* 4.4 2.1 - - - -
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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