Contacts of the helix formed by residues 628 - 637 (chain B) in PDB entry 1P48
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 PRO 628 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B ASN 4.9 0.2 - - - +
627B VAL* 1.3 93.4 - - + +
629B LEU* 1.3 66.1 + - - +
630B TYR* 3.4 34.5 - - + +
631B LYS* 3.0 19.4 + - + +
632B HIS* 3.2 9.4 + - - +
918B GLU* 3.6 21.5 - - - +
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Residues in contact with LEU 629 (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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618B SER* 3.9 32.5 - - - +
619B ARG* 4.0 29.8 - - + +
622B ALA* 4.0 10.9 - - + +
627B VAL 3.7 1.4 + - - -
628B PRO* 1.3 71.5 - - - +
630B TYR* 1.3 57.9 + - - +
632B HIS* 3.1 3.4 + - + -
633B LEU* 2.9 43.9 + - + +
882B PHE* 3.9 27.1 - - + -
885B ASP* 3.3 33.2 + - + +
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Residues in contact with TYR 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B PRO* 3.4 24.4 - - + +
629B LEU* 1.3 74.6 - - - +
631B LYS* 1.3 72.0 + - + +
633B LEU* 3.5 1.7 + - - -
634B ALA* 3.1 23.0 + - - +
644B TYR* 3.7 26.1 - + - -
885B ASP* 3.1 51.5 + - - +
888B VAL* 3.8 18.4 - - + -
889B GLY* 3.4 10.9 - - - -
915B ILE* 3.8 25.6 - - + -
918B GLU* 2.5 32.0 + - - +
919B LEU* 3.4 39.1 - - + +
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Residues in contact with LYS 631 (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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627B VAL* 3.7 25.8 - - + -
628B PRO* 3.0 23.9 + - + +
630B TYR* 1.3 82.9 - - + +
632B HIS* 1.3 65.6 + - - +
634B ALA* 3.2 3.4 + - - +
635B ASP* 3.1 46.7 + - - +
641B THR* 4.2 20.2 + - + +
644B TYR* 3.3 25.5 + - - +
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Residues in contact with HIS 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B VAL 4.8 0.8 + - - -
584B LYS* 4.1 9.7 + - + -
586B GLN* 5.1 0.2 + - - -
618B SER* 3.3 29.6 - - - -
621B ALA* 3.3 23.7 - - + +
622B ALA* 3.8 23.3 - - + -
625B LYS* 3.0 33.3 + - + +
627B VAL* 4.1 4.9 - - + -
628B PRO 3.2 2.5 + - - +
629B LEU* 3.1 7.9 + - + +
631B LYS* 1.3 80.5 - - - +
633B LEU* 1.3 60.3 + - + +
635B ASP* 3.2 7.4 + - - +
636B LEU* 2.9 65.9 + - + +
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Residues in contact with LEU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B SER* 4.4 3.1 - - - +
629B LEU* 2.9 36.6 + - + +
630B TYR 3.8 5.2 - - - +
632B HIS* 1.3 76.4 - - + +
634B ALA* 1.3 63.0 + - - +
636B LEU* 3.5 11.9 + - + +
637B SER* 2.9 28.3 + - - -
852B LEU* 4.0 21.8 - - + -
856B ILE* 5.0 3.1 - - + +
882B PHE* 3.9 29.6 - - + -
885B ASP* 3.6 7.2 - - + +
886B LEU* 3.5 41.5 - - + +
889B GLY* 4.2 10.2 - - - -
890B LEU* 5.3 1.4 - - + +
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Residues in contact with ALA 634 (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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630B TYR 3.1 14.1 + - - +
631B LYS* 3.5 10.5 - - - +
632B HIS 3.2 0.2 - - - -
633B LEU* 1.3 77.2 - - - +
635B ASP* 1.3 57.6 + - - +
637B SER* 3.3 1.6 + - - -
638B LYS* 2.8 23.9 + - - -
639B SER* 2.8 16.4 + - - +
640B LYS 5.2 0.2 - - - +
641B THR* 3.6 30.7 - - + -
644B TYR* 4.6 3.4 - - + -
889B GLY* 3.4 22.4 + - - +
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Residues in contact with ASP 635 (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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625B LYS* 2.9 31.3 + - - +
631B LYS* 3.1 46.6 + - - +
632B HIS* 3.2 7.3 + - + +
634B ALA* 1.3 79.0 - - - +
636B LEU* 1.3 63.9 + - + +
638B LYS* 3.0 19.6 + - - +
641B THR* 5.2 1.0 - - - +
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Residues in contact with LEU 636 (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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584B LYS 3.7 9.4 - - - +
586B GLN* 3.6 43.1 - - + +
587B LYS* 5.6 5.2 - - - -
632B HIS* 2.9 55.0 + - + +
633B LEU* 3.8 11.0 - - + +
635B ASP* 1.3 78.2 - - + +
637B SER* 1.3 58.9 + - - +
638B LYS* 3.7 5.7 + - - +
852B LEU* 3.9 17.7 - - + -
856B ILE* 4.0 17.7 - - + +
860B GLN* 4.6 2.6 + - - -
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Residues in contact with SER 637 (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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633B LEU 2.9 17.9 + - - -
634B ALA* 3.3 3.8 + - - -
636B LEU* 1.3 76.3 - - - +
638B LYS* 1.3 70.0 + - - +
639B SER* 2.7 26.5 + - - -
856B ILE* 3.6 22.0 - - - -
860B GLN* 3.1 24.4 + - - +
889B GLY 3.8 3.3 + - - -
890B LEU* 3.8 16.1 - - - +
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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