Contacts of the helix formed by residues 642 - 650 (chain B) in PDB entry 3JUE
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 GLY 642 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B ILE* 4.5 0.2 - - - -
634B ASN* 4.8 3.8 - - - -
635B GLN 3.8 10.1 - - - -
636B ALA* 3.8 5.4 - - - +
640B GLY 3.6 3.0 + - - -
641B ARG* 1.3 72.3 - - - +
643B PRO* 1.3 71.2 - - - +
644B LEU 3.3 2.7 - - - -
645B HIS* 3.1 16.7 + - - -
646B HIS* 3.0 31.8 + - - -
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Residues in contact with PRO 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B THR* 5.4 0.4 - - - +
611B LEU* 3.8 25.8 - - + -
612B ILE* 4.3 13.4 - - + -
615B THR* 4.0 4.4 - - - +
632B ASN 4.8 0.7 - - - +
633B VAL 3.2 28.0 - - - +
634B ASN 4.5 0.4 - - - -
635B GLN 3.4 17.5 - - - +
642B GLY* 1.3 82.5 - - - +
644B LEU* 1.3 57.8 + - - +
646B HIS* 3.4 7.6 + - + +
647B ALA 2.8 24.6 + - - -
659B PHE* 3.4 38.3 - - + -
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B VAL 4.9 1.6 + - - +
634B ASN* 6.1 0.4 - - - +
642B GLY 3.3 1.0 - - - -
643B PRO* 1.3 76.0 - - - +
645B HIS* 1.3 68.3 + - + +
647B ALA* 3.2 1.3 + - - -
648B THR* 3.0 33.5 + - - +
656B ALA* 4.0 38.1 - - + +
659B PHE* 3.8 7.9 - - + +
660B LEU* 3.9 24.0 - - + -
664B ALA* 4.3 17.0 - - + -
665B ASP 3.9 16.8 - - - +
666B LEU* 4.5 2.7 - - - -
676B PRO* 3.5 29.8 - - + -
692B LEU* 4.1 12.8 - - + -
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Residues in contact with HIS 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B GLY 3.8 14.5 + - - -
641B ARG* 4.0 17.3 - - + -
642B GLY* 3.1 25.0 + - - +
644B LEU* 1.3 78.6 - - + +
646B HIS* 1.3 58.0 + - - +
648B THR* 3.3 4.2 + - - -
649B ILE* 2.9 32.7 + - + +
665B ASP 5.7 0.2 - - - -
668B ALA* 2.7 46.6 + - + -
669B ARG 4.5 0.2 - - - -
670B ASP* 3.8 8.6 + - + -
674B ARG 3.0 20.2 + - - -
676B PRO* 3.7 16.8 - - + +
679B ILE* 3.6 24.6 - - + +
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Residues in contact with HIS 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ILE* 3.8 30.7 + - + +
615B THR* 3.9 15.5 - - + -
616B ALA* 5.7 2.9 - - - +
637B ASP* 2.8 29.6 + - - -
641B ARG* 3.2 36.8 + - + +
642B GLY 3.0 28.6 + - - -
643B PRO* 3.8 7.6 - - + +
645B HIS* 1.3 76.4 - - - +
647B ALA* 1.3 62.7 + - - +
649B ILE* 3.4 10.1 + - - +
650B LEU* 3.1 36.2 + - + +
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Residues in contact with ALA 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B THR* 3.6 16.0 - - + +
643B PRO 2.8 21.1 + - - +
644B LEU 3.2 3.8 + - - +
646B HIS* 1.3 72.7 - - - +
648B THR* 1.3 56.9 + - - +
650B LEU* 3.4 1.5 + - - -
651B GLY 3.0 8.0 + - - -
652B HIS* 2.8 37.4 + - + +
655B LEU* 4.0 7.0 - - + -
656B ALA* 3.8 31.4 - - - +
659B PHE* 4.1 3.1 - - + -
688B ILE* 4.8 1.6 - - - -
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Residues in contact with THR 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B LEU* 3.0 23.0 + - - +
645B HIS* 3.6 4.9 - - - -
647B ALA* 1.3 74.0 - - - +
649B ILE* 1.3 66.1 + - - +
651B GLY* 3.0 13.3 + - - -
656B ALA* 4.8 0.3 - - - +
676B PRO* 3.6 21.6 - - - +
679B ILE* 3.8 8.7 - - + -
680B ALA* 3.4 41.5 - - + +
683B THR* 4.4 9.9 + - - +
685B ASN* 5.2 1.1 + - + -
688B ILE* 3.9 23.8 - - + +
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Residues in contact with ILE 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641B ARG* 3.9 33.9 - - - +
645B HIS 2.9 29.4 + - - +
646B HIS* 3.8 11.9 - - - +
648B THR* 1.3 72.0 - - - +
650B LEU* 1.3 73.0 + - + +
651B GLY 3.5 0.2 + - - -
674B ARG* 4.1 15.9 - - - +
679B ILE* 3.8 25.4 - - + -
683B THR* 4.6 12.0 - - + +
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Residues in contact with LEU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B THR* 4.0 4.0 - - + +
616B ALA* 3.7 34.5 - - + +
646B HIS* 3.1 27.2 + - + +
647B ALA 4.1 0.4 - - - +
648B THR 3.2 0.2 - - - -
649B ILE* 1.3 88.4 - - + +
651B GLY* 1.3 62.6 + - - +
652B HIS* 3.5 35.5 + - + +
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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