Contacts of the strand formed by residues 508 - 514 (chain D) in PDB entry 1T5A
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 VAL 508 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406C SER* 4.8 11.0 - - - +
408C PRO* 4.7 16.4 - - + -
423D CYS* 4.1 23.1 - - + +
425D SER* 3.5 4.6 - - - -
426D GLY* 3.1 24.1 + - - -
506D GLY 4.5 4.3 - - - +
507D ASP* 1.3 77.1 - - - +
509D VAL* 1.3 72.5 + - - +
527D VAL* 3.2 33.4 - - + -
528D VAL 3.4 9.4 - - - +
529D PRO* 4.7 7.2 - - + -
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Residues in contact with VAL 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D SER* 4.1 1.8 - - - -
426D GLY 4.3 0.2 - - - +
427D ALA* 3.2 23.6 - - + +
429D ILE* 3.7 25.1 - - + -
494D MET* 5.0 4.3 - - + -
503D PHE* 3.9 25.6 - - + -
508D VAL* 1.3 80.3 - - - +
510D ILE* 1.3 81.1 + - - +
511D VAL* 3.9 3.5 + - + -
526D ARG 3.6 0.3 - - - +
527D VAL* 3.7 2.4 - - - -
528D VAL* 2.8 37.7 + - - +
530D VAL* 3.8 23.6 - - + -
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Residues in contact with ILE 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416D ALA* 4.0 20.0 - - + +
419D ALA* 4.4 4.9 - - + -
420D SER* 3.9 15.7 - - - +
423D CYS* 4.0 19.5 - - - -
425D SER* 3.8 17.5 - - - +
427D ALA 3.0 6.6 + - - +
428D ILE* 3.2 11.2 - - + -
429D ILE 2.7 32.2 + - - -
509D VAL* 1.3 83.3 - - - +
511D VAL* 1.3 57.7 + - - +
525D MET* 3.4 33.2 - - + -
526D ARG 3.5 1.6 - - - -
527D VAL* 3.7 28.5 - - + -
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Residues in contact with VAL 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D ILE* 3.4 18.4 - - + +
490D VAL* 3.7 43.5 - - + -
494D MET* 4.8 2.2 - - + -
509D VAL* 4.3 7.6 - - + +
510D ILE* 1.3 80.7 - - - +
512D LEU* 1.3 66.3 + - - +
513D THR* 4.0 11.2 + - + -
524D THR 3.4 5.2 - - - +
525D MET* 3.5 2.4 - - - -
526D ARG* 2.9 45.4 + - + +
528D VAL* 3.8 30.1 - - + -
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Residues in contact with LEU 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D THR 6.0 0.2 - - - +
412D THR* 3.5 27.1 - - + -
413D ALA* 4.6 8.1 - - + -
416D ALA* 3.9 23.1 - - + -
428D ILE* 4.6 3.6 - - + -
429D ILE 2.7 15.8 + - - +
430D VAL* 4.0 20.9 - - + -
431D LEU* 3.2 24.1 + - - +
437D SER* 4.9 2.5 - - - +
441D VAL* 3.5 32.1 - - + -
510D ILE* 4.3 0.4 - - + -
511D VAL* 1.3 72.3 - - - +
513D THR* 1.3 69.0 + - - +
522D THR* 4.3 15.7 - - + -
524D THR 3.5 7.4 - - - +
525D MET* 3.9 11.2 - - + -
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Residues in contact with THR 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431D LEU* 4.4 4.7 - - + -
486D VAL* 4.1 19.3 - - + -
490D VAL* 4.2 5.8 - - + -
511D VAL* 4.0 10.5 - - + -
512D LEU* 1.3 80.4 - - - +
514D GLY* 1.3 60.6 + - - +
522D THR* 3.3 9.1 - - - +
523D ASN 3.0 20.4 + - - -
524D THR* 3.0 26.7 + - - +
526D ARG* 3.6 23.7 + - - +
532D FBP 4.2 9.6 - - - -
706D GOL 3.4 23.5 + - - -
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Residues in contact with GLY 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D TRP* 3.5 8.2 - - - -
486D VAL* 6.3 0.2 - - - +
513D THR* 1.3 77.1 - - - +
515D TRP* 1.3 59.8 + - - -
516D ARG 3.6 0.2 - - - -
521D PHE 3.0 16.8 - - - -
522D THR* 3.8 1.6 - - - -
523D ASN* 3.9 6.1 - - - -
524D THR* 4.4 1.7 + - - -
532D FBP 2.9 26.6 + - - -
706D GOL 2.9 22.9 + - - -
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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