Contacts of the helix formed by residues 625 - 637 (chain B) in PDB entry 5IWM
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 VAL 625 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B GLU* 5.5 4.9 + - - +
620B MET* 4.5 2.3 - - - +
623B GLY* 3.4 2.0 - - - -
624B ASP* 1.3 85.1 - - - +
626B VAL* 1.3 63.7 + - - +
627B GLU* 3.5 13.4 + - + +
628B ASN* 3.6 38.9 + - - +
629B ARG* 3.8 16.0 + - - -
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Residues in contact with VAL 626 (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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178A GLY* 3.8 31.0 - - - +
179A MET* 4.7 0.7 - - - +
624B ASP 3.2 11.2 + - - +
625B VAL* 1.3 70.7 - - - +
627B GLU* 1.3 60.0 + - - +
629B ARG* 3.3 21.9 + - - +
630B ARG* 2.8 26.2 + - + +
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Residues in contact with GLU 627 (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 VAL* 3.4 10.8 - - + +
626B VAL* 1.3 78.8 - - - +
628B ASN* 1.3 56.0 + - - +
630B ARG* 2.7 46.6 + - - +
631B GLN* 2.7 38.9 + - + +
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Residues in contact with ASN 628 (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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619B GLU 5.8 0.8 + - - -
620B MET* 3.9 28.3 - - + +
625B VAL* 3.6 32.8 + - - +
626B VAL 3.4 0.4 - - - -
627B GLU* 1.3 78.3 - - - +
629B ARG* 1.3 57.7 + - - +
631B GLN* 3.3 8.0 + - - +
632B PHE* 2.9 28.4 + - - +
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Residues in contact with ARG 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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22A PHE* 3.8 24.9 - - + -
177A VAL* 4.0 16.5 - - + +
178A GLY* 4.6 8.1 - - - +
466B LYS* 3.9 19.6 - - - +
620B MET* 3.5 27.7 + - - +
621B LEU* 2.9 31.5 + - + +
622B MET 4.0 0.6 - - - -
623B GLY 2.7 30.7 + - - +
624B ASP* 4.2 2.6 + - - +
625B VAL 3.8 5.3 + - - +
626B VAL* 3.3 34.7 + - - +
627B GLU 3.2 0.2 - - - -
628B ASN* 1.3 77.0 - - - +
630B ARG* 1.3 63.4 + - - +
632B PHE* 3.4 7.8 + - + +
633B ILE* 3.1 33.1 + - + +
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Residues in contact with ARG 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLY* 3.4 31.2 - - - +
179A MET* 4.4 14.8 - - + +
626B VAL* 2.8 13.3 + - + +
627B GLU* 2.7 42.9 + - - +
629B ARG* 1.3 75.9 - - - +
631B GLN* 1.3 82.3 + - - +
633B ILE* 3.4 4.9 + - - +
634B GLU* 2.8 49.5 + - + +
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Residues in contact with GLN 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 GLU* 2.7 23.5 + - + +
628B ASN* 3.3 9.2 + - - +
630B ARG* 1.3 94.9 + - - +
632B PHE* 1.3 63.8 + - - +
634B GLU* 3.5 11.1 + - - +
635B ASP* 2.8 60.8 + - - +
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Residues in contact with PHE 632 (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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19A ARG* 3.7 53.8 - - + -
22A PHE* 5.1 3.1 - + - -
23A LEU* 3.6 32.8 - - + -
620B MET* 3.8 27.6 - - + -
621B LEU* 3.7 20.0 - - + -
628B ASN 2.9 16.1 + - - +
629B ARG* 3.7 6.3 - - + +
630B ARG 3.3 0.2 - - - -
631B GLN* 1.3 76.3 - - - +
633B ILE* 1.3 73.0 + - + +
635B ASP* 4.9 1.1 - - - -
636B ASN* 3.1 60.1 + - + +
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Residues in contact with ILE 633 (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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22A PHE* 5.8 1.3 - - + -
23A LEU* 3.9 13.5 - - + -
26A ALA* 4.1 18.8 - - + -
27A MET* 5.0 3.8 - - + -
30A ILE* 3.8 23.6 - - + -
177A VAL* 3.5 35.2 - - + +
178A GLY* 4.0 8.1 - - - -
179A MET* 4.8 7.0 - - + -
629B ARG* 3.1 20.2 + - + +
630B ARG* 3.7 6.3 - - - +
632B PHE* 1.3 82.8 - - + +
634B GLU* 1.3 57.4 + - - +
637B ALA* 2.8 46.8 + - + +
639B TYR* 4.8 5.8 - - - +
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Residues in contact with GLU 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 ARG* 2.8 50.9 + - - +
631B GLN* 3.8 12.2 + - - +
633B ILE* 1.3 82.7 - - - +
635B ASP* 1.3 71.7 + - - +
636B ASN 3.3 0.5 + - - -
637B ALA* 3.8 11.0 + - - +
639B TYR* 5.9 1.5 - - - -
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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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631B GLN* 2.8 48.7 + - - +
632B PHE* 4.1 3.8 - - - +
634B GLU* 1.3 83.4 - - - +
636B ASN* 1.3 69.9 + - - +
637B ALA 5.5 0.2 - - - -
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Residues in contact with ASN 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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19A ARG* 4.9 3.8 - - - +
23A LEU* 3.4 27.4 - - + +
632B PHE* 3.1 52.3 + - + +
635B ASP* 1.3 89.5 - - - +
637B ALA* 1.3 65.9 + - - +
638B VAL* 3.4 12.1 + - - +
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Residues in contact with ALA 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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23A LEU* 4.3 6.3 - - + +
27A MET* 3.3 29.6 - - + -
633B ILE* 2.8 23.1 + - + +
634B GLU* 3.8 8.3 + - - +
635B ASP 5.5 0.2 - - - -
636B ASN* 1.3 77.8 - - - +
638B VAL* 1.3 61.3 + - - +
639B TYR* 3.7 26.0 + - + +
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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