Contacts of the strand formed by residues 624 - 629 (chain D) 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 ILE 624 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461D HIS* 3.9 6.4 - - - -
531D SER* 5.1 10.3 - - - +
534D GLU* 4.7 7.4 - - + -
535D MET* 4.6 13.7 - - + -
538D ARG* 3.6 20.9 - - - +
590D ILE* 3.3 19.5 - - + +
592D VAL* 4.4 20.0 - - + -
615D ILE* 4.2 21.1 - - + -
619D ALA* 3.0 39.3 + - + +
622D ALA* 3.4 30.7 - - + +
623D GLY* 1.3 78.4 - - - +
625D HIS* 1.3 66.7 + - - +
626D LEU* 4.9 0.2 - - + -
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Residues in contact with HIS 625 (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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439D VAL* 5.0 1.1 - - + -
456D LEU* 3.4 38.5 - - + +
457D ALA* 3.6 26.1 + - + +
460D PRO* 3.1 31.8 - - + +
461D HIS* 4.1 1.3 - - - -
589D THR* 3.8 17.7 - - + +
590D ILE 3.2 13.9 + - - +
591D VAL* 4.6 5.0 - - + +
592D VAL* 2.8 27.8 + - - +
619D ALA 5.1 0.4 - - - -
620D ARG 4.5 8.8 + - - -
623D GLY* 3.7 23.8 - - - -
624D ILE* 1.3 79.5 + - - +
626D LEU* 1.3 70.1 + - - +
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Residues in contact with LEU 626 (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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456D LEU* 4.8 1.0 - - - +
460D PRO 4.3 0.2 + - - -
461D HIS* 3.5 26.3 + - + +
462D LEU 3.0 24.4 + - - -
528D LEU* 6.1 1.1 - - + -
592D VAL* 3.3 19.1 - - + +
594D VAL* 5.7 1.1 - - + -
612D ILE* 3.7 47.3 - - + +
615D ILE* 3.6 27.8 - - + -
616D ALA* 5.1 4.3 - - + -
624D ILE* 4.9 1.6 - - + -
625D HIS* 1.3 84.1 - - - +
627D ILE* 1.3 69.6 + - - +
628D LEU* 3.8 24.2 - - + -
646D ILE* 5.1 0.7 - - + -
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Residues in contact with ILE 627 (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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441D LEU* 4.7 5.8 - - + -
456D LEU* 3.7 30.3 - - + -
462D LEU* 3.7 20.6 - - + -
464D VAL* 4.7 8.3 - - + -
476D VAL* 4.8 17.3 - - + -
479D MET* 4.0 25.8 - - + -
480D LEU* 6.1 0.2 - - + -
591D VAL* 4.4 8.5 - - + -
592D VAL 3.2 6.9 + - - -
593D VAL* 3.7 27.6 - - + -
594D VAL 2.9 30.3 + - - +
626D LEU* 1.3 81.0 - - - +
628D LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 628 (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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462D LEU 2.8 15.9 + - - +
463D LEU* 3.4 10.2 - - + -
464D VAL* 2.7 34.2 + - - +
594D VAL* 3.7 30.1 - - + -
597D PHE* 3.7 31.8 - - + -
612D ILE* 4.0 16.8 - - + -
626D LEU* 3.8 31.0 - - + -
627D ILE* 1.3 71.8 - - - +
629D ALA* 1.3 55.1 + - - +
642D ILE* 4.3 6.3 - - + -
646D ILE* 3.7 29.4 - - + -
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Residues in contact with ALA 629 (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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464D VAL* 3.3 21.1 - - + -
472D LYS* 4.8 7.4 - - + +
476D VAL* 4.1 21.1 - - + -
594D VAL 3.3 13.0 + - - +
595D ASP* 3.3 22.7 - - - +
596D GLU* 3.3 0.2 - - - -
597D PHE* 3.2 27.0 + - - -
627D ILE* 5.0 1.1 - - + +
628D LEU* 1.3 75.0 - - - +
630D THR* 1.3 61.1 + - - +
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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