Contacts of the helix formed by residues 639 - 646 (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 THR 639 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D MET* 4.9 3.1 - - - -
609D GLU* 2.8 35.6 + - - +
635D VAL* 3.8 11.2 - - - +
636D ASP 3.8 14.1 - - - +
637D VAL 3.2 13.0 + - - +
638D ILE* 1.3 77.2 - - - +
640D GLY* 1.3 63.4 + - - +
641D LEU* 3.3 6.0 + - - -
642D ILE* 3.4 19.7 + - - +
643D LYS* 3.3 26.3 + - - +
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Residues in contact with GLY 640 (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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635D VAL* 6.1 0.4 - - - +
639D THR* 1.3 72.9 - - - +
641D LEU* 1.3 60.7 + - - +
643D LYS* 3.2 16.2 + - - +
644D ALA 2.9 24.3 + - - -
632E ARG* 3.0 36.5 + - - -
636E ASP* 5.4 1.1 - - - -
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Residues in contact with LEU 641 (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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606D LYS* 4.1 14.4 - - - +
609D GLU* 3.4 37.0 - - + +
610D GLU* 5.7 2.0 - - + -
613D ALA* 4.5 19.0 - - + +
639D THR* 3.3 0.6 - - - +
640D GLY* 1.3 77.7 - - - +
642D ILE* 1.3 63.7 + - + +
644D ALA* 3.5 10.2 + - - +
645D ASN* 3.7 18.9 + - - +
602E MET* 3.7 35.5 - - + +
632E ARG* 4.3 10.8 - - - +
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Residues in contact with ILE 642 (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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463D LEU* 3.9 23.1 - - + -
597D PHE* 4.7 8.7 - - + -
601D MET* 4.6 12.6 - - + -
609D GLU* 4.6 16.2 - - + +
612D ILE* 3.8 31.0 - - + -
613D ALA 5.0 1.8 - - - +
628D LEU* 4.3 5.6 - - + -
637D VAL 4.6 6.7 - - - +
638D ILE* 4.8 4.5 - - + -
639D THR* 3.4 28.9 + - - +
640D GLY 3.3 0.6 - - - -
641D LEU* 1.3 81.0 - - + +
643D LYS* 1.3 60.8 + - - +
644D ALA 3.4 0.5 + - - -
645D ASN* 4.9 0.2 - - - +
646D ILE* 3.4 43.4 + - + +
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Residues in contact with LYS 643 (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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463D LEU* 5.2 1.8 - - + -
635D VAL* 6.0 5.1 - - - +
638D ILE* 3.7 19.2 + - + -
639D THR 3.3 22.6 + - - +
640D GLY* 3.2 15.9 + - - +
642D ILE* 1.3 75.5 - - - +
644D ALA* 1.3 65.0 + - - +
646D ILE 3.5 14.6 - - - +
647D PRO* 5.3 0.7 - - - +
649D ARG* 3.3 29.8 + - - +
661D ARG 5.8 0.2 + - - -
662D THR* 4.0 22.3 + - - +
665D ASP* 4.2 16.9 + - - +
632E ARG* 5.5 2.7 - - - +
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Residues in contact with ALA 644 (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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640D GLY 2.9 15.8 + - - +
641D LEU* 3.8 7.4 - - - +
642D ILE 3.3 0.8 - - - -
643D LYS* 1.3 79.7 - - - +
645D ASN* 1.3 68.0 + - - +
646D ILE 5.3 0.3 - - - -
647D PRO* 5.8 0.2 - - - +
598E ALA* 5.7 5.6 - - + -
599E ASP* 5.3 4.0 - - - +
602E MET* 5.3 3.8 - - - -
631E GLN* 5.7 2.3 - - - +
632E ARG* 3.6 32.9 - - + +
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Residues in contact with ASN 645 (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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460D PRO* 5.4 0.5 - - - +
461D HIS* 4.0 6.4 - - - -
613D ALA* 3.5 6.4 - - - +
616D ALA* 3.3 31.1 + - + +
617D GLN* 3.5 23.1 + - - +
641D LEU 3.7 8.7 + - - +
642D ILE 3.8 2.0 + - - -
644D ALA* 1.3 79.7 + - - +
646D ILE* 1.3 62.6 + - + +
647D PRO* 3.3 11.8 - - - +
500E LYS* 4.8 10.0 + - - +
599E ASP* 3.0 27.0 + - - -
602E MET* 3.4 28.6 - - - +
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Residues in contact with ILE 646 (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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461D HIS* 3.7 30.3 - - + -
462D LEU 3.9 6.1 - - - +
463D LEU* 3.8 21.1 - - + -
612D ILE* 5.0 3.6 - - + -
616D ALA* 4.1 17.0 - - + -
626D LEU* 5.1 1.3 - - + -
628D LEU* 3.7 31.2 - - + -
642D ILE* 3.4 30.2 + - + +
643D LYS* 3.5 11.3 - - - +
644D ALA 3.5 1.2 - - - -
645D ASN* 1.3 81.0 - - + +
647D PRO* 1.3 61.7 - - - +
648D THR 3.8 13.7 - - - +
649D ARG* 3.4 15.9 + - - -
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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