Contacts of the helix formed by residues 689 - 706 (chain B) in PDB entry 2FH2
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 GLN 689 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647B ASN* 3.0 35.2 + - - +
687B ASP 5.2 3.1 - - - +
688B SER* 1.3 79.7 + - - +
690B GLU* 1.3 66.3 + - - +
691B GLU* 3.8 14.0 - - - +
692B GLU* 3.0 35.1 + - + +
693B LYS* 3.4 5.5 + - - +
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Residues in contact with GLU 690 (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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688B SER 4.1 1.0 + - - -
689B GLN* 1.3 72.8 - - - +
691B GLU* 1.3 70.3 + - - +
693B LYS* 3.3 31.5 + - - +
694B THR* 3.2 31.1 + - - +
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Residues in contact with GLU 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B ASN* 4.3 13.9 - - - +
652B PHE* 5.3 0.2 - - - -
689B GLN* 3.1 12.4 - - + +
690B GLU* 1.3 88.9 + - - +
692B GLU* 1.3 63.3 + - - +
694B THR* 3.4 8.7 + - - -
695B GLU* 3.2 27.7 + - - +
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Residues in contact with GLU 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B CYS 4.4 6.7 - - - +
646B SER* 3.3 3.2 - - - -
647B ASN* 3.0 50.8 + - + +
652B PHE* 4.1 13.6 - - + -
669B ASP 3.1 6.5 - - - +
670B ASP* 3.3 8.6 - - - +
671B VAL* 3.8 16.2 - - + +
688B SER* 3.6 1.6 - - - -
689B GLN* 3.0 35.2 + - + +
691B GLU* 1.3 75.2 - - - +
693B LYS* 1.3 63.4 + - - +
696B ALA* 3.1 24.9 + - - +
2003B CA 2.4 31.2 - - - -
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Residues in contact with LYS 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B VAL* 3.8 14.9 - - + +
682B VAL* 5.0 3.3 - - + +
684B VAL* 4.1 30.5 - - + +
688B SER* 5.7 0.4 - - - +
689B GLN 3.4 4.8 + - - +
690B GLU* 3.3 35.6 + - - +
692B GLU* 1.3 77.1 - - - +
694B THR* 1.3 64.3 + - - +
696B ALA* 3.4 3.6 + - - +
697B LEU* 3.0 45.3 + - + +
719B VAL* 4.3 21.3 - - + +
721B LYS* 5.8 4.6 - - - +
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Residues in contact with THR 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B GLU* 3.2 24.2 + - - +
691B GLU* 3.7 11.6 - - - -
692B GLU 3.3 0.2 - - - -
693B LYS* 1.3 79.0 - - - +
695B GLU* 1.3 63.2 + - + +
697B LEU* 3.6 10.7 + - - +
698B THR* 2.9 30.9 + - - +
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Residues in contact with GLU 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B ARG* 5.8 2.3 + - - -
652B PHE* 3.3 51.7 - - + +
691B GLU 3.2 14.9 + - - +
694B THR* 1.3 81.1 - - + +
696B ALA* 1.3 56.2 + - - +
697B LEU 3.3 0.4 - - - -
698B THR* 3.2 16.7 + - + +
699B SER* 2.7 36.0 + - - -
702B ARG* 5.0 6.2 + - - -
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Residues in contact with ALA 696 (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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645B CYS* 4.1 7.2 - - - -
652B PHE* 3.8 7.5 - - - -
671B VAL* 3.6 28.0 - - + -
673B LEU* 3.8 19.4 - - + +
682B VAL* 4.2 3.4 - - + -
692B GLU 3.1 21.1 + - - +
693B LYS 3.7 2.9 - - - +
695B GLU* 1.3 74.9 - - - +
697B LEU* 1.3 60.4 + - - +
699B SER* 3.2 5.5 + - - -
700B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B VAL* 4.0 14.4 - - + -
693B LYS* 3.0 41.8 + - + +
694B THR* 3.8 8.7 - - - +
696B ALA* 1.3 77.0 - - - +
698B THR* 1.3 58.9 + - - +
700B ALA* 3.2 5.2 + - - +
701B LYS* 3.0 29.5 + - - +
717B ILE* 3.9 30.8 - - + +
719B VAL* 4.0 15.7 - - + -
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Residues in contact with THR 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B THR* 2.9 21.2 + - - +
695B GLU* 3.2 22.5 + - + +
696B ALA 3.2 0.4 - - - -
697B LEU* 1.3 80.2 - - - +
699B SER* 1.3 56.4 + - - +
701B LYS* 3.6 11.3 - - + +
702B ARG* 3.1 33.2 + - - +
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Residues in contact with SER 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B CYS* 5.5 0.2 - - - -
652B PHE* 3.5 5.4 - - - -
654B ILE* 3.3 32.1 - - - +
673B LEU* 4.1 10.5 - - - -
695B GLU 2.7 20.2 + - - -
696B ALA* 3.6 7.4 - - - -
698B THR* 1.3 75.1 - - - +
700B ALA* 1.3 54.0 + - - +
701B LYS 3.2 0.4 - - - -
702B ARG* 3.2 22.7 + - - +
703B TYR* 2.8 41.4 + - - -
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Residues in contact with ALA 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B LEU* 4.1 9.6 - - + +
680B VAL* 3.9 24.1 - - + +
682B VAL* 4.3 12.3 - - + -
696B ALA 2.9 16.3 + - - +
697B LEU* 3.2 6.0 + - - +
699B SER* 1.3 76.2 - - - +
701B LYS* 1.3 62.4 + - - +
703B TYR* 3.4 5.0 + - - +
704B ILE* 3.2 30.5 + - - +
717B ILE* 3.8 17.7 - - + -
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Residues in contact with LYS 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU 3.0 16.5 + - - +
698B THR* 3.6 11.9 - - + +
700B ALA* 1.3 78.3 - - - +
702B ARG* 1.3 59.9 + - - +
704B ILE* 3.7 3.9 + - - +
705B GLU* 3.0 57.9 + - - +
717B ILE* 4.0 11.8 - - + +
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Residues in contact with ARG 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B PHE* 5.3 2.6 - - - -
654B ILE* 3.8 24.0 - - - +
695B GLU* 5.0 7.5 + - - -
698B THR* 3.1 24.5 + - + +
699B SER* 3.2 29.9 + - - +
701B LYS* 1.3 75.7 - - - +
703B TYR* 1.3 74.1 + - - +
705B GLU* 4.5 4.5 - - - +
706B THR* 2.8 37.0 + - - +
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Residues in contact with TYR 703 (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* 6.2 0.9 - - - -
643B PHE* 3.7 42.5 - + - -
654B ILE* 3.8 19.2 - - + +
673B LEU* 4.1 25.1 - - + -
675B ASP* 5.1 7.2 - - - +
680B VAL* 6.0 3.4 - - + -
699B SER* 2.8 33.9 + - - +
700B ALA* 3.9 6.1 - - - +
702B ARG* 1.3 84.8 + - - +
704B ILE* 1.3 65.0 + - + +
705B GLU 3.5 0.2 + - - -
706B THR* 3.7 16.0 + - - -
707B ASP 5.0 0.5 + - - -
711B ARG* 4.2 17.9 + - - +
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Residues in contact with ILE 704 (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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680B VAL* 3.7 29.8 - - + -
700B ALA 3.2 18.0 + - - +
701B LYS* 3.9 5.2 - - - +
702B ARG 3.2 0.2 - - - -
703B TYR* 1.3 79.4 - - - +
705B GLU* 1.3 65.1 + - + +
706B THR 3.8 0.2 + - - -
707B ASP 4.4 4.0 + - - +
708B PRO* 4.8 1.0 - - - +
711B ARG* 3.3 35.7 - - - +
712B ASP 4.1 19.1 - - - +
713B ARG* 5.1 7.2 - - - -
715B THR* 4.1 26.5 - - + +
717B ILE* 3.8 25.1 - - + -
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Residues in contact with GLU 705 (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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701B LYS* 3.0 58.6 + - - +
702B ARG* 4.3 4.1 - - - +
703B TYR 3.3 0.2 - - - -
704B ILE* 1.3 83.2 - - + +
706B THR* 1.3 65.7 + - - +
707B ASP 3.3 3.2 + - - -
708B PRO* 3.7 21.9 - - + +
713B ARG* 6.5 1.3 - - + -
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Residues in contact with THR 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ARG* 2.8 29.5 + - - +
703B TYR* 3.9 14.3 + - - -
704B ILE 3.5 1.2 - - - -
705B GLU* 1.3 77.1 - - - +
707B ASP* 1.3 63.0 + - + +
708B PRO* 3.9 4.3 - - - +
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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