Contacts of the helix formed by residues 635 - 649 (chain G) in PDB entry 3HR4
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 CYS 635 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592G THR* 3.0 15.2 + - - -
625G GLY* 3.0 38.4 - - - -
626G LEU 3.6 13.5 - - - -
627G GLY 3.8 3.6 - - - -
633G ARG 3.6 0.6 + - - -
634G PHE* 1.3 92.6 - - - +
636G ALA* 1.3 59.8 + - - +
637G PHE 3.3 0.7 - - - -
638G ALA* 3.5 2.3 + - + +
639G HIS* 2.9 28.6 + - - +
656G MET* 3.9 13.2 - - + -
658G GLU* 3.7 11.7 - - - +
659G GLY 4.4 2.2 - - - -
999G FMN 2.9 13.9 + - - -
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Residues in contact with ALA 636 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592G THR* 3.2 3.0 + - - +
596G GLY* 3.5 15.5 - - - +
633G ARG* 3.1 38.6 - - + -
634G PHE 3.0 3.5 - - - -
635G CYS* 1.3 76.2 - - - +
637G PHE* 1.3 61.4 + - - +
639G HIS* 3.2 8.7 + - - +
640G ASP* 2.8 34.8 + - - +
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Residues in contact with PHE 637 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544G ALA* 4.5 0.7 - - + -
572G MET* 3.6 24.0 - - + -
590G THR* 3.2 32.1 - - + -
591G SER 3.6 1.8 - - - +
592G THR* 3.3 9.7 + - - +
596G GLY 3.7 4.7 + - - +
597G ASP 3.7 18.8 - - - +
598G CYS* 3.6 26.9 - - + -
599G PRO* 3.6 15.5 - - + -
602G GLY* 5.0 2.7 - - - -
605G LEU* 5.6 0.7 - - + -
606G LYS* 4.3 25.6 - - + -
610G PHE* 5.4 1.8 - + - -
636G ALA* 1.3 75.1 - - - +
638G ALA* 1.3 66.4 + - - +
640G ASP* 2.9 30.2 + - + +
641G ILE* 3.2 32.5 + - + +
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Residues in contact with ALA 638 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590G THR* 3.7 23.8 - - + +
592G THR* 4.1 1.6 + - - -
623G VAL* 3.9 7.0 - - + +
625G GLY* 3.5 33.0 - - - +
635G CYS* 3.6 10.0 - - + +
637G PHE* 1.3 79.9 - - - +
639G HIS* 1.3 50.5 + - - +
641G ILE* 3.1 6.7 + - - +
642G ASP* 2.7 34.3 + - - +
656G MET* 3.8 13.0 - - + -
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Residues in contact with HIS 639 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634G PHE 3.9 12.3 - - - -
635G CYS 2.9 22.4 + - - +
636G ALA* 3.4 9.9 - - - +
638G ALA* 1.3 75.1 - - - +
640G ASP* 1.3 53.5 + - - +
642G ASP* 3.7 11.5 + - - -
643G GLN* 2.8 46.6 + - - +
656G MET* 3.7 32.8 + - + +
658G GLU* 4.1 12.2 + - - +
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Residues in contact with ASP 640 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596G GLY 3.9 8.8 - - - +
606G LYS* 4.0 9.2 + - - -
610G PHE* 3.6 37.3 - - + -
636G ALA* 2.8 24.0 + - - +
637G PHE* 2.9 20.8 + - + +
639G HIS* 1.3 72.8 - - - +
641G ILE* 1.3 51.9 + - + +
643G GLN* 3.6 3.5 - - - +
644G LYS* 2.6 38.6 + - - +
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Residues in contact with ILE 641 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572G MET* 4.3 8.5 - - + -
588G VAL* 4.3 31.9 - - + -
590G THR* 4.4 2.7 - - + -
605G LEU* 5.2 4.0 - - + -
609G LEU* 4.2 23.1 - - + -
610G PHE* 6.1 1.3 - - + -
623G VAL* 4.7 4.0 - - + -
637G PHE* 3.5 45.3 - - + +
638G ALA* 3.1 6.2 + - - +
640G ASP* 1.3 75.6 - - + +
642G ASP* 1.3 57.0 + - - +
643G GLN 3.0 4.5 - - - -
644G LYS* 4.0 5.2 - - - -
645G LEU* 2.8 57.4 + - + +
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Residues in contact with ASP 642 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621G TYR* 3.1 28.0 + - - -
623G VAL* 3.8 16.0 + - + +
638G ALA 2.7 20.3 + - - +
639G HIS* 4.1 11.8 + - - +
641G ILE* 1.3 72.8 - - - +
643G GLN* 1.3 61.3 + - - +
645G LEU 4.2 0.2 - - - -
646G SER* 3.7 6.1 + - - -
652G GLN* 2.9 25.1 + - - +
656G MET* 2.9 45.8 + - + +
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Residues in contact with GLN 643 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639G HIS* 2.8 25.8 + - - +
640G ASP* 3.8 4.0 - - - +
642G ASP* 1.3 79.7 - - - +
644G LYS* 1.3 62.7 + - - +
645G LEU 3.2 1.9 + - - -
646G SER* 3.5 9.2 + - - -
647G HIS* 3.5 52.8 + - + +
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Residues in contact with LYS 644 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609G LEU* 3.4 57.2 + - + +
610G PHE* 5.4 7.9 - - + +
612G LEU* 3.1 27.7 + - - +
640G ASP 2.6 25.9 + - - +
641G ILE* 3.1 3.6 + - - +
643G GLN* 1.3 74.1 - - - +
645G LEU* 1.3 62.5 + - + +
647G HIS* 4.0 6.1 + - - +
648G LEU* 3.1 58.4 + - - +
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Residues in contact with LEU 645 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580G LEU* 5.4 6.1 - - + -
586G LEU* 4.9 10.1 - - + -
588G VAL* 5.2 0.7 - - + -
609G LEU* 4.7 10.1 - - + -
619G PHE* 4.3 18.6 - - + -
621G TYR* 3.6 47.3 - - + -
623G VAL* 4.7 2.5 - - + -
641G ILE* 2.8 40.5 + - + +
644G LYS* 1.3 87.7 - - + +
646G SER* 1.3 65.8 + - - +
647G HIS 3.2 0.4 - - - -
648G LEU* 3.3 25.0 + - + +
649G GLY 3.3 0.2 + - - -
650G ALA* 3.2 26.1 + - + +
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Residues in contact with SER 646 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C ASP* 3.9 8.1 - - - +
621G TYR* 3.4 21.2 + - - -
642G ASP 3.7 10.2 + - - -
643G GLN* 3.5 15.7 + - - -
644G LYS 3.5 0.4 - - - -
645G LEU* 1.3 78.8 - - - +
647G HIS* 1.3 64.8 + - - +
649G GLY* 3.1 14.2 + - - -
650G ALA 4.1 7.6 + - - +
652G GLN* 5.4 0.2 - - - -
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Residues in contact with HIS 647 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C ASP* 3.5 15.7 - - - +
643G GLN* 3.5 44.0 + - + +
644G LYS* 4.3 6.3 - - - +
645G LEU 3.2 0.6 - - - -
646G SER* 1.3 77.8 - - - +
648G LEU* 1.3 59.1 + - + +
649G GLY 2.8 11.1 + - - -
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Residues in contact with LEU 648 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C ASP* 5.7 0.2 - - - -
580G LEU* 6.1 2.0 - - + -
609G LEU* 5.1 0.9 - - + -
612G LEU* 4.6 9.0 - - + -
613G LYS* 4.1 26.0 - - - +
614G GLU* 4.1 4.0 - - - +
615G LEU* 3.4 43.9 + - + +
618G LYS* 3.2 21.0 + - - -
644G LYS* 3.1 53.3 + - - +
645G LEU* 3.3 20.7 + - + +
647G HIS* 1.3 78.5 - - + +
649G GLY* 1.3 57.7 + - - +
650G ALA 3.6 0.4 - - - -
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Residues in contact with GLY 649 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682C GLU 5.7 0.5 - - - +
685C ASP* 4.3 19.0 - - - +
618G LYS* 4.1 22.2 - - - +
645G LEU 3.3 0.2 + - - -
646G SER 3.1 9.8 + - - -
647G HIS 2.8 7.0 + - - -
648G LEU* 1.3 80.2 - - - +
650G ALA* 1.3 69.3 + - - +
651G SER* 3.3 7.1 + - - -
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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
------------------------------------------------------------
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