Contacts of the strand formed by residues 440 - 445 (chain D) in PDB entry 6T8G
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 PRO 440 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D TYR* 3.8 25.8 - - + -
435D HIS* 3.6 27.4 - - + +
437D SER 3.4 14.1 - - - +
438D THR 3.5 5.6 - - - +
439D VAL* 1.3 89.2 - - - +
441D LEU* 1.3 70.0 + - - +
442D ALA 3.8 0.9 - - - -
453D ILE* 3.7 15.0 - - + -
454D THR 4.0 5.4 - - - +
455D ASP* 4.7 0.2 - - - -
482D SER* 3.4 25.1 - - - +
483D ILE* 3.8 2.6 - - + +
486D LYS* 4.3 11.0 - - + -
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Residues in contact with LEU 441 (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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440D PRO* 1.3 81.9 - - - +
442D ALA* 1.3 59.4 + - - +
443D LEU* 3.0 23.1 + - + +
453D ILE* 4.2 2.4 - - - +
454D THR* 3.2 26.6 + - - +
456D LEU* 3.7 43.7 - - + -
459D MET* 4.2 2.0 - - + -
462D LEU* 3.8 18.6 - - + -
479D MET* 3.6 50.9 - - + +
482D SER* 4.0 2.5 - - - -
483D ILE* 4.0 13.7 - - + -
627D ILE* 4.3 2.7 - - + -
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Residues in contact with ALA 442 (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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423D PHE* 4.5 6.3 - - + -
426D VAL* 3.7 19.7 - - + +
427D LEU* 3.8 17.5 - - + -
432D TYR* 4.7 2.5 - - + -
440D PRO 3.8 1.2 - - - -
441D LEU* 1.3 69.5 - - - +
443D LEU* 1.3 64.4 - - - +
444D GLY 3.7 0.4 - - - -
453D ILE* 3.7 28.8 - - + +
478D ALA* 4.4 12.1 - - - +
482D SER* 3.3 25.8 + - - +
694D ALA* 5.9 0.3 - - - +
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Residues in contact with LEU 443 (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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426D VAL* 4.7 1.1 - - - -
441D LEU* 3.0 18.1 + - + +
442D ALA* 1.3 77.2 - - - +
444D GLY* 1.3 59.6 + - - +
452D ILE* 3.3 12.4 + - + +
454D THR* 4.2 11.4 - - + +
462D LEU* 6.2 1.1 - - + -
475D GLY 5.5 0.2 - - - +
478D ALA* 5.5 4.6 - - + +
479D MET* 3.8 26.5 - - + -
650D ILE* 4.9 4.3 - - + -
678D MET* 3.7 38.7 - - + +
680D TYR* 3.8 35.0 - - + -
691D VAL* 4.5 11.9 - - + -
692D HIS 3.2 12.0 - - - +
693D GLY* 3.2 15.8 - - - -
694D ALA* 3.3 7.8 + - - +
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Residues in contact with GLY 444 (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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421D VAL* 4.9 0.2 - - - -
426D VAL* 3.8 25.7 - - - +
442D ALA 3.7 0.8 - - - -
443D LEU* 1.3 85.1 - - - +
445D HIS* 1.3 63.3 + - - -
451D PRO* 3.6 2.3 - - - +
452D ILE* 2.8 37.7 + - - +
691D VAL* 5.0 1.9 - - - +
692D HIS 3.3 6.7 - - - -
694D ALA 4.7 1.1 - - - -
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Residues in contact with HIS 445 (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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363D PRO* 4.7 9.9 - - + -
421D VAL* 3.5 36.5 - - + +
425D GLU* 3.4 52.4 + - + +
426D VAL* 4.3 4.7 - - + +
444D GLY* 1.3 74.1 - - - -
446D ASP* 1.3 69.4 + - - +
449D GLY* 2.6 32.6 + - - -
450D ARG 3.2 6.0 - - - +
451D PRO* 3.9 12.0 - - + +
691D VAL* 3.3 4.7 - - - +
692D HIS* 2.9 35.1 + - + -
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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