Contacts of the strand formed by residues 589 - 594 (chain B) in PDB entry 6T8O
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 589 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B THR* 4.3 7.2 + - - -
439B VAL* 4.4 23.8 - - + -
491B GLU 3.2 22.6 + - - -
492B ALA* 3.4 7.8 - - - +
493B ARG* 2.7 34.0 + - - +
550B LEU* 4.0 17.2 - - + +
554B ASN* 5.5 0.2 + - - -
587B LEU 3.6 1.5 + - - -
588B PRO* 1.3 72.0 - - - +
590B ILE* 1.3 63.6 + - - +
591B VAL* 4.7 2.5 - - + -
623B GLY* 3.6 16.2 - - - +
625B HIS* 4.0 16.8 - - + +
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Residues in contact with ILE 590 (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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493B ARG* 3.8 13.7 - - + -
495B ILE* 3.9 28.3 - - + +
514B LEU* 3.7 24.2 - - + -
530B TRP* 5.4 7.9 - - + -
531B SER* 5.4 1.6 - - - +
534B GLU* 5.5 2.7 - - + -
538B ARG* 3.7 14.8 - - - +
588B PRO* 3.5 22.6 + - + +
589B THR* 1.3 79.1 - - - +
591B VAL* 1.3 65.5 + - - +
592B VAL* 3.9 13.7 - - + -
623B GLY 2.9 11.0 + - - +
624B ILE* 3.3 20.1 - - + -
625B HIS 2.9 25.6 + - - -
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Residues in contact with VAL 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B VAL* 4.7 10.3 - - + -
456B LEU* 4.0 24.2 - - + -
480B LEU* 5.2 2.9 - - + -
483B ILE* 5.0 7.6 - - + -
492B ALA* 6.3 0.2 - - + -
493B ARG 3.7 7.3 + - - +
494B LEU* 3.7 25.7 - - + +
495B ILE 3.1 22.6 + - - +
589B THR* 4.7 8.3 - - + +
590B ILE* 1.3 80.3 - - - +
592B VAL* 1.3 64.2 + - - +
593B VAL* 4.0 6.8 + - + +
625B HIS* 3.4 12.6 - - + +
627B ILE* 3.7 31.4 - - + +
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Residues in contact with VAL 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 3.3 24.5 - - + +
497B ILE* 4.3 19.1 - - + -
528B LEU* 4.3 13.7 - - + -
531B SER* 4.4 8.3 - - - +
590B ILE* 3.9 20.2 - - + -
591B VAL* 1.3 74.8 - - - +
593B VAL* 1.3 71.3 + - - +
594B VAL* 4.7 2.2 - - + -
624B ILE* 4.4 14.1 - - + -
625B HIS 3.0 6.2 + - - +
626B LEU* 3.4 27.4 - - + +
627B ILE 3.0 23.4 + - - +
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Residues in contact with VAL 593 (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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476B VAL* 5.2 4.3 - - + -
480B LEU* 4.3 24.5 - - + -
494B LEU* 6.1 0.2 - - + -
495B ILE 3.1 7.6 + - - +
496B MET* 3.7 32.7 - - + -
497B ILE* 3.0 26.9 + - - +
504B LEU* 4.1 22.2 - - + -
591B VAL* 4.6 5.4 - - + +
592B VAL* 1.3 78.5 - - - +
594B VAL* 1.3 70.5 + - - +
627B ILE* 3.3 33.7 - - + +
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Residues in contact with VAL 594 (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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497B ILE* 3.3 35.4 - - + +
499B PRO* 4.7 3.4 - - + -
504B LEU* 5.9 0.4 - - - -
528B LEU* 5.6 7.0 - - + -
592B VAL* 4.4 6.9 + - + -
593B VAL* 1.3 82.1 - - - +
595B ASP* 1.3 62.2 + - - +
596B GLU 3.9 3.6 - - - +
597B PHE* 3.5 36.1 - - + +
600B MET* 5.3 7.6 - - + -
612B ILE* 5.6 3.8 - - + -
626B LEU* 5.5 0.4 - - + -
627B ILE 3.6 4.8 + - - +
628B LEU* 4.1 22.8 - - + +
629B ALA* 2.8 31.1 + - - +
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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