Contacts of the helix formed by residues 637 - 647 (chain D) in PDB entry 2FGJ
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 ASP 637 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502C GLY 4.1 8.1 - - - +
503C ARG* 3.7 19.8 - - + +
504C SER* 2.8 37.1 + - - +
662C ALA* 4.2 11.8 - - + +
701C LEU* 5.2 5.0 - - + +
802C ATP 5.7 1.0 + - - +
635D ALA 4.1 1.6 + - - -
636D LEU* 1.3 73.8 - - - +
638D TYR* 1.3 66.0 - - - +
639D GLU* 3.0 15.1 + - - +
640D SER* 2.6 53.4 + - - -
641D GLU* 3.1 10.9 + - - +
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Residues in contact with TYR 638 (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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662C ALA 3.4 16.3 + - - -
663C ARG* 3.1 17.2 - - - +
664C LEU* 2.9 48.6 + - + +
665C SER* 4.4 2.9 + - - -
701C LEU* 3.3 33.5 - - + +
702C TYR* 5.3 0.9 - - - -
704C LEU* 3.9 26.8 - - + +
705C GLN* 3.1 49.3 + - + +
637D ASP* 1.3 72.0 - - - +
639D GLU* 1.3 56.8 + - - +
641D GLU* 3.8 1.4 + - - +
642D HIS* 3.1 28.2 + - - +
663D ARG* 3.5 19.3 - - - +
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Residues in contact with GLU 639 (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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503C ARG* 3.1 33.1 + - - +
700C TYR* 3.1 35.9 + - + +
701C LEU* 5.0 6.3 - - + +
704C LEU* 4.2 11.8 - - + +
637D ASP* 3.1 10.3 + - - +
638D TYR* 1.3 76.2 - - - +
640D SER* 1.3 64.7 + - - +
642D HIS* 3.3 9.1 + - + +
643D VAL* 3.2 31.0 + - + +
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Residues in contact with SER 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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503C ARG* 5.6 0.3 - - - +
504C SER* 4.0 1.9 + - - -
582D ALA 4.8 1.0 - - - +
583D GLY* 5.6 0.7 - - - -
613D ARG* 3.8 29.1 + - - +
636D LEU* 3.7 18.4 - - - -
637D ASP* 2.6 34.6 + - - -
639D GLU* 1.3 75.5 - - - +
641D GLU* 1.3 61.1 + - - +
643D VAL* 3.6 9.3 + - - +
644D ILE* 3.5 24.6 + - - +
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Residues in contact with GLU 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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705C GLN* 4.3 8.5 - - - +
633D THR* 3.1 30.8 + - + +
636D LEU* 3.6 15.1 - - + +
637D ASP 3.1 14.2 + - - +
638D TYR 4.0 2.7 - - - +
640D SER* 1.3 74.3 - - - +
642D HIS* 1.3 56.1 + - - +
643D VAL 3.2 0.4 - - - -
644D ILE* 3.1 6.2 + - - +
645D MET* 2.8 47.7 + - + +
663D ARG* 2.5 33.2 + - - +
666D THR* 2.7 37.3 + - - +
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Residues in contact with HIS 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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704C LEU* 4.8 19.9 - - + +
705C GLN* 5.8 0.4 - - - +
638D TYR 3.1 20.5 + - - +
639D GLU* 3.3 11.0 + - + +
641D GLU* 1.3 78.0 - - - +
643D VAL* 1.3 53.6 - - + +
645D MET* 4.5 6.4 - - - +
646D ARG* 2.7 70.2 + - + +
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Residues in contact with VAL 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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580D LYS 4.5 2.5 - - - +
583D GLY* 3.9 27.4 - - - +
639D GLU* 3.2 20.5 + - + +
640D SER* 3.7 11.7 - - - +
641D GLU 3.2 0.2 - - - -
642D HIS* 1.3 77.7 - - + +
644D ILE* 1.3 61.6 + - - +
646D ARG* 3.5 4.4 + - - +
647D ASN* 3.1 37.7 + - - +
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Residues in contact with ILE 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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581D LEU 4.0 6.1 - - - +
582D ALA* 3.2 33.7 - - - +
613D ARG* 4.1 4.3 - - + -
616D ILE* 3.8 28.3 - - + -
629D PHE* 4.3 13.9 - - + -
633D THR* 4.3 8.1 - - + -
636D LEU* 3.7 22.7 - - + -
640D SER 3.5 14.8 + - - +
641D GLU* 3.1 5.9 + - - +
643D VAL* 1.3 76.1 - - - +
645D MET* 1.3 60.8 + - + +
647D ASN 3.3 1.7 + - - -
648D MET* 3.0 31.9 + - + +
651D ILE* 3.4 21.7 - - + +
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Residues in contact with MET 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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497D VAL* 5.6 1.8 - - + -
629D PHE* 5.4 3.6 - - - -
633D THR* 5.4 3.6 - - + -
641D GLU* 2.8 42.4 + - + +
642D HIS* 4.1 7.6 - - - +
644D ILE* 1.3 73.9 - - + +
646D ARG* 1.3 60.8 + - - +
648D MET* 3.0 51.1 - - + +
649D HIS 4.6 0.5 + - - -
659D ILE* 3.8 24.9 - - + -
666D THR* 3.3 33.2 - - - +
667D VAL* 5.3 0.9 - - - -
669D ASN* 6.0 6.5 - - + -
670D ALA 6.4 0.2 - - - +
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Residues in contact with ARG 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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642D HIS* 2.7 54.2 + - + +
643D VAL* 3.9 5.8 - - - +
645D MET* 1.3 72.6 - - - +
647D ASN* 1.3 61.7 + - - +
648D MET 3.2 1.0 + - - -
649D HIS* 4.2 10.6 + - - +
650D LYS* 5.8 2.3 - - - +
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Residues in contact with ASN 647 (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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580D LYS 3.6 15.4 + - - -
581D LEU* 3.3 38.8 + - + +
643D VAL* 3.1 24.8 + - - +
644D ILE 3.4 6.7 - - - +
645D MET 3.2 0.2 - - - -
646D ARG* 1.3 76.3 - - - +
648D MET* 1.3 50.9 + - - +
649D HIS 3.2 3.4 - - - -
650D LYS* 3.0 23.8 + - + +
651D ILE* 2.8 38.2 + - + +
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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