Contacts of the strand formed by residues 461 - 465 (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 HIS 461 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456D LEU* 4.9 1.3 - - - -
459D MET* 3.4 4.0 - - - +
460D PRO* 1.3 102.2 + - + +
462D LEU* 1.3 64.7 + - - +
615D ILE* 4.2 2.0 - - + -
616D ALA* 3.4 36.0 + - + +
619D ALA* 3.3 33.8 - - + +
624D ILE 4.1 6.3 - - - -
626D LEU* 3.3 35.4 - - + +
645D ASN* 5.1 0.7 - - + -
646D ILE* 3.7 35.8 - - + +
647D PRO* 4.5 2.2 - - + +
648D THR* 3.3 25.3 + - - +
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Residues in contact with LEU 462 (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* 3.8 18.2 - - + -
443D LEU* 6.2 1.3 - - + -
456D LEU* 4.0 2.9 - - + -
459D MET* 3.7 29.6 - - + -
461D HIS* 1.3 77.8 - - - +
463D LEU* 1.3 59.4 + - - +
464D VAL* 3.7 25.8 - - + -
479D MET* 3.7 16.6 - - + -
626D LEU 3.4 5.1 + - - +
627D ILE* 3.7 23.1 - - + -
628D LEU* 3.1 27.4 + - - +
646D ILE* 4.0 4.4 - - - +
648D THR* 3.3 11.9 - - + +
650D ILE* 3.7 24.5 - - + -
680D TYR* 5.6 0.4 - - + -
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Residues in contact with LEU 463 (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* 1.3 74.9 - - - +
464D VAL* 1.3 79.9 + - - +
597D PHE* 4.5 5.8 - - + -
628D LEU* 4.3 14.6 - - + -
630D THR* 4.0 11.0 - - + -
638D ILE* 3.7 40.8 - - + -
642D ILE* 4.0 22.2 - - + +
643D LYS* 5.2 2.9 - - + -
646D ILE* 4.1 13.7 - - + +
648D THR 3.3 6.0 + - - +
649D ARG* 3.6 23.9 - - + +
650D ILE* 2.7 32.1 + - - +
663D ILE* 3.7 11.7 - - + -
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Residues in contact with VAL 464 (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* 3.7 20.4 - - + -
463D LEU* 1.3 82.0 - - - +
465D ALA* 1.3 63.9 + - - +
472D LYS* 4.5 17.9 - - + +
475D GLY* 6.5 0.2 - - - -
476D VAL* 5.5 4.9 - - + -
479D MET* 4.5 10.5 - - + -
627D ILE* 5.2 1.6 - - + -
628D LEU 3.3 22.0 + - - +
629D ALA* 3.3 6.8 - - + -
630D THR* 2.9 29.7 + - - +
650D ILE* 3.3 13.7 - - + +
652D PHE* 3.6 30.1 - - + -
678D MET* 6.4 0.2 - - + -
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Residues in contact with ALA 465 (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* 1.3 76.7 - - - +
466D GLY* 1.3 59.5 + - - +
472D LYS* 4.3 3.1 - - - -
630D THR* 3.4 21.1 - - + +
633D PRO* 4.1 16.2 - - + -
650D ILE 3.2 7.8 + - - +
651D ALA* 5.1 0.9 - - - -
652D PHE* 2.9 35.1 + - - -
654D VAL* 4.6 7.2 - - + -
663D ILE* 3.7 25.4 - - + -
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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