Contacts of the strand formed by residues 594 - 602 (chain B) in PDB entry 6AHU
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 LYS 594 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450B ALA* 3.4 16.1 - - + +
451B SER* 2.6 50.2 + - - +
452B VAL* 4.8 0.2 - - - +
455B VAL* 3.8 28.7 - - + +
464B HIS* 5.0 5.9 - - + +
466B TRP* 3.2 20.8 - - - -
467B TRP* 3.4 40.6 - - + +
508B THR* 3.8 12.6 - - + +
509B VAL 4.1 4.5 - - - -
510B GLY* 4.7 2.7 - - - -
592B GLU* 3.2 30.0 + - + +
593B SER* 1.3 71.6 - - - +
595B ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B HIS* 4.6 10.1 - - + -
466B TRP* 3.7 21.5 - - + -
508B THR* 4.2 0.2 - - - -
509B VAL* 2.9 25.3 + - - +
562B VAL* 3.8 28.0 - - + +
593B SER* 3.2 12.8 + - - +
594B LYS* 1.3 80.0 - - - +
596B PRO* 1.3 77.6 - - + +
597B ILE* 4.7 2.2 - - + +
623B PRO* 5.0 4.3 - - + -
626B TRP* 3.6 39.0 - - + +
630B PHE* 3.7 27.1 - - + -
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Residues in contact with PRO 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B TRP* 4.1 17.3 - - + -
507B LEU 3.4 17.3 - - - +
508B THR* 3.8 19.3 - - + +
509B VAL 4.0 0.2 - - - +
550B HIS 5.8 0.9 - - - +
552B PHE* 3.8 33.0 - - + +
553B ILE* 3.3 33.6 - - + +
558B ILE* 6.3 0.4 - - + -
562B VAL* 5.6 2.9 - - + -
594B LYS 4.2 0.7 - - - +
595B ILE* 1.3 96.5 - - + +
597B ILE* 1.3 69.7 + - - +
623B PRO* 4.2 4.3 - - - +
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Residues in contact with ILE 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B ILE* 5.2 9.4 - - + -
506B GLY* 3.7 2.4 - - - -
507B LEU* 3.2 27.4 + - + +
509B VAL* 3.7 29.8 - - + -
550B HIS 5.6 0.3 - - - +
551B SER* 6.0 1.0 - - - -
552B PHE 6.0 0.5 + - - -
553B ILE* 4.8 7.9 - - - +
595B ILE* 4.7 4.9 - - + +
596B PRO* 1.3 83.6 - - - +
598B LEU* 1.3 65.3 + - - +
599B LEU* 3.8 35.2 - - + -
620B VAL* 4.3 10.1 - - + -
621B LEU 3.3 8.1 - - - +
622B LEU* 3.7 29.2 - - + -
630B PHE* 4.2 18.8 - - + -
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Residues in contact with LEU 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ILE* 5.5 3.1 - - + -
504B ILE* 3.7 23.1 - - + -
506B GLY* 3.7 22.9 - - - +
549B THR* 5.6 0.2 - - + -
551B SER* 4.3 18.8 - - - +
553B ILE* 4.8 7.9 - - + -
554B TRP* 4.6 17.9 - - + +
597B ILE* 1.3 76.6 - - - +
599B LEU* 1.3 67.7 + - - +
600B ILE* 3.8 27.1 - - + -
619B ASP 3.2 4.1 - - - +
620B VAL* 3.3 4.9 - - - -
621B LEU* 2.9 64.3 + - + +
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Residues in contact with LEU 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B LEU* 3.8 35.4 - - + -
447B ILE* 5.2 2.7 - - + -
487B PHE* 3.9 22.4 - - + -
490B LEU* 5.0 4.0 - - + -
503B THR 3.7 0.9 - - - +
504B ILE* 3.6 1.6 - - - -
505B LEU* 3.0 50.9 + - + +
506B GLY* 5.7 0.2 - - - -
507B LEU* 4.9 4.9 - - + -
597B ILE* 3.8 19.3 - - + -
598B LEU* 1.3 78.3 - - - +
600B ILE* 1.3 65.9 + - - +
618B TRP* 4.1 16.6 - - + -
619B ASP 3.5 1.3 - - - +
620B VAL* 3.7 28.5 - - + -
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Residues in contact with ILE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B GLN* 3.4 34.5 - - + +
311B ILE* 3.8 26.0 - - + -
330B TRP* 4.1 12.8 - - + -
502B GLY 4.5 0.4 - - - +
503B THR 3.4 9.2 - - - +
504B ILE* 3.7 23.1 - - + -
598B LEU* 3.8 25.4 - - + -
599B LEU* 1.3 78.6 - - - +
601B GLN* 1.3 62.1 + - - +
618B TRP* 3.2 3.8 - - - -
619B ASP* 2.4 55.6 + - + +
621B LEU* 5.8 1.6 - - + -
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Residues in contact with GLN 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B GLN* 3.9 0.3 + - - -
496B PRO* 3.9 9.2 - - + +
499B ILE* 3.4 45.8 + - + +
501B ALA* 3.9 0.8 - - - +
502B GLY* 3.0 51.1 - - - +
503B THR* 3.5 25.3 + - + +
600B ILE* 1.3 79.9 - - - +
602B GLN* 1.3 84.6 + - - +
603B PRO* 3.7 4.9 - - - +
617B GLY 3.3 8.2 + - - +
618B TRP* 3.6 30.9 - - + +
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Residues in contact with GLN 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B GLN* 4.0 17.6 - - - +
309B THR* 4.7 13.0 - - - +
330B TRP* 5.2 0.4 - - - -
431B ARG* 3.1 18.8 - - - +
433B ARG* 3.6 28.5 + - - +
600B ILE* 5.1 0.2 - - + -
601B GLN* 1.3 85.6 - - - +
603B PRO* 1.3 68.9 - - + +
615B GLY 3.1 6.3 - - - +
616B SER* 3.6 2.6 - - - -
617B GLY* 2.6 37.8 + - - +
619B ASP* 2.9 27.5 + - - +
650B HIS* 5.2 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