Contacts of the helix formed by residues 637 - 651 (chain B) in PDB entry 3H44
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 LYS 637 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B GLU 4.1 12.7 + - - -
530B PHE* 3.4 45.3 - - + +
531B ILE 3.4 18.4 + - - -
532B PRO* 4.9 1.1 - - + +
533B THR* 4.1 6.8 + - - +
616B LEU* 3.8 11.4 - - + +
634B TYR* 4.1 4.0 + - - +
636B ASP* 1.3 102.1 - - + +
638B GLN* 1.3 65.0 + - - +
639B PRO 3.3 2.7 - - - -
640B ILE* 2.9 31.3 + - + +
641B LEU 3.3 7.6 + - - -
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Residues in contact with GLN 638 (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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572B ALA* 2.9 47.9 + - - +
574B LEU* 3.6 24.7 - - + +
616B LEU* 3.8 10.4 - - + +
631B VAL* 3.7 21.0 + - + +
632B LYS 3.5 7.3 + - - -
633B GLY 3.4 25.9 + - - +
634B TYR 3.8 2.8 + - - +
635B ASN* 3.2 17.6 + - - +
637B LYS* 1.3 76.6 - - - +
639B PRO* 1.3 73.0 - - + +
641B LEU* 3.2 3.1 + - - +
642B LEU* 3.1 25.5 + - - +
741B ILE* 5.7 0.9 - - + +
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Residues in contact with PRO 639 (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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635B ASN 3.6 8.1 - - - +
636B ASP 4.0 5.8 - - - +
637B LYS 3.7 1.6 - - - -
638B GLN* 1.3 97.3 - - + +
640B ILE* 1.3 66.8 + - + +
642B LEU* 3.9 5.9 - - + +
643B LYS* 3.0 26.7 + - - +
741B ILE* 4.5 22.0 - - + -
744B MET* 4.0 21.3 - - + +
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Residues in contact with ILE 640 (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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530B PHE* 4.6 8.1 - - + -
607B TYR* 3.3 22.2 - - - +
637B LYS* 2.9 34.4 + - + +
639B PRO* 1.3 77.8 - - + +
641B LEU* 1.3 59.5 + - - +
643B LYS* 3.6 4.6 - - - +
644B LYS* 3.0 26.2 + - + +
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Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B PHE* 4.5 7.0 - - + -
604B LEU* 5.6 1.3 - - + -
607B TYR* 3.8 27.1 - - + -
608B ALA* 4.8 14.6 - - + -
611B ALA* 4.7 8.3 - - + -
616B LEU* 3.9 33.2 - - + +
617B SER* 4.6 6.1 - - - -
618B TYR* 4.4 13.5 - - + +
631B VAL* 4.3 16.6 - - + -
637B LYS 3.3 1.2 + - - +
638B GLN 3.2 5.1 + - - +
640B ILE* 1.3 79.5 - - - +
642B LEU* 1.3 67.4 + - - +
644B LYS* 3.0 5.8 + - + -
645B ILE* 2.9 42.1 + - + +
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Residues in contact with LEU 642 (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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574B LEU* 4.7 10.1 - - + -
576B PHE* 4.6 7.9 - - + -
629B LEU* 3.9 20.4 - - + -
631B VAL* 4.5 13.6 - - + +
638B GLN 3.1 17.4 + - - +
639B PRO* 3.9 5.2 - - + +
641B LEU* 1.3 75.6 - - - +
643B LYS* 1.3 63.4 + - - +
645B ILE* 2.9 21.5 + - + +
646B ILE* 3.1 35.9 + - + +
741B ILE* 3.8 21.3 - - + -
744B MET* 4.3 11.7 - - + -
745B VAL* 3.6 28.0 - - + -
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Residues in contact with LYS 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B PRO 3.0 17.0 + - - +
640B ILE* 3.6 5.2 - - - +
642B LEU* 1.3 79.1 - - - +
644B LYS* 1.3 65.0 + - - +
646B ILE* 3.4 5.3 + - - +
647B GLU* 2.9 56.7 + - + +
744B MET* 3.5 36.2 - - + +
748B THR* 5.1 10.5 - - + +
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B LEU* 4.5 13.4 - - + +
607B TYR* 4.0 55.3 - - + +
640B ILE* 3.0 15.6 + - + +
641B LEU* 3.0 8.0 + - + +
643B LYS* 1.3 74.5 - - - +
645B ILE* 1.3 52.3 + - - +
647B GLU* 3.3 18.8 - - - +
648B LYS* 2.7 51.3 + - + +
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Residues in contact with ILE 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B LEU* 5.1 1.1 - - + +
604B LEU* 3.5 31.0 - - + -
618B TYR* 3.6 33.0 - - + -
620B LEU* 4.9 6.1 - - + -
629B LEU* 4.6 17.9 - - + -
631B VAL* 4.7 3.6 - - + -
641B LEU* 2.9 36.0 + - + +
642B LEU* 2.9 12.9 + - + +
644B LYS* 1.3 72.0 - - - +
646B ILE* 1.3 64.6 + - + +
648B LYS* 2.8 3.5 + - - +
649B MET* 2.7 57.6 + - + +
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Residues in contact with ILE 646 (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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576B PHE* 6.4 0.2 - - + -
578B PHE* 4.3 17.5 - - + -
629B LEU* 4.5 9.2 - - + -
642B LEU* 3.1 33.5 + - + +
643B LYS* 4.1 5.2 - - - +
645B ILE* 1.3 75.4 - - + +
647B GLU* 1.3 63.5 + - - +
649B MET* 3.7 15.8 - - - +
650B ALA* 2.9 24.8 + - - +
744B MET* 6.3 0.7 - - - -
745B VAL* 3.9 28.9 - - + +
748B THR* 3.7 26.2 - - - +
749B LEU* 3.9 26.7 - - + -
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Residues in contact with GLU 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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643B LYS* 2.9 49.8 + - + +
644B LYS* 3.3 20.4 - - - +
646B ILE* 1.3 81.0 - - - +
648B LYS* 1.3 60.1 + - - +
649B MET 3.1 0.6 + - - -
650B ALA* 3.3 1.0 + - - +
651B THR* 2.8 32.1 + - + +
748B THR* 3.9 20.2 - - + +
752B HIS* 4.4 15.0 + - + +
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Residues in contact with LYS 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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600B LEU* 3.4 16.3 - - + +
603B SER* 3.0 31.9 + - - -
604B LEU* 3.8 33.0 - - + +
644B LYS* 2.7 35.5 + - + +
645B ILE* 3.6 3.8 - - - +
647B GLU* 1.3 73.8 - - - +
649B MET* 1.3 57.3 + - - +
651B THR* 3.8 7.4 + - - +
652B PHE* 3.1 38.0 + - + +
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Residues in contact with MET 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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578B PHE* 5.5 7.2 - - + -
596B TYR* 2.8 32.2 + - - +
597B LEU* 4.6 5.8 - - + -
600B LEU* 3.2 33.0 - - + -
620B LEU* 3.8 28.7 - - + -
627B MET* 5.2 11.0 - - + +
629B LEU* 5.6 1.1 - - + -
645B ILE* 2.7 19.6 + - + +
646B ILE* 3.7 26.9 - - + +
648B LYS* 1.3 77.2 - - - +
650B ALA* 1.3 63.0 + - + +
651B THR 3.1 5.5 + - - -
652B PHE* 3.6 9.5 + - - +
716B ILE* 4.5 2.8 - - - +
720B LEU* 3.8 15.7 - - + +
749B LEU* 5.3 4.5 - - + -
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Residues in contact with ALA 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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646B ILE 2.9 16.1 + - - +
647B GLU* 4.2 1.1 - - - +
649B MET* 1.3 76.6 - - - +
651B THR* 1.3 60.1 + - - +
652B PHE 3.7 0.4 - - - -
716B ILE* 6.3 0.2 - - - -
720B LEU* 3.7 11.7 - - - +
748B THR 4.5 3.6 - - - +
749B LEU* 4.0 15.5 - - + -
752B HIS* 3.6 36.8 - - + +
753B ALA* 3.9 18.8 - - + +
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Residues in contact with THR 651 (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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647B GLU* 2.8 24.9 + - + +
648B LYS* 3.8 5.7 + - - +
650B ALA* 1.3 81.3 - - - +
652B PHE* 1.3 68.4 + - - +
653B GLU* 3.4 16.6 + - - +
752B HIS* 3.1 38.1 - - + +
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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
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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