Contacts of the helix formed by residues 627 - 632 (chain B) in PDB entry 1XR2
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 ILE 627 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B PHE* 4.7 1.6 - - + -
582B ARG* 3.7 31.6 - - + +
592B TRP* 3.9 12.3 - - + -
596B PHE* 4.1 11.2 - - + -
621B TYR* 3.7 35.2 - - + -
623B ASP 4.8 3.1 - - - +
624B PHE* 3.9 20.2 - - + +
626B GLU* 1.3 85.0 - - + +
628B ILE* 1.3 58.4 + - - +
629B GLU* 3.2 3.4 - - - -
630B TYR* 2.7 34.7 + - + +
631B ILE* 2.9 35.0 + - + +
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Residues in contact with ILE 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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160A ASN* 4.8 8.1 - - + +
624B PHE* 2.8 24.0 + - + +
625B ASN* 4.5 6.3 - - - +
627B ILE* 1.3 76.0 - - - +
629B GLU* 1.3 68.7 + - + +
631B ILE* 4.2 8.1 - - + -
632B HIS* 3.0 22.3 + - - +
653B ALA* 3.7 30.5 - - + +
654B PHE* 4.4 8.1 - - + -
657B PHE* 3.7 26.4 - - + -
660B TRP* 3.4 36.1 - - + -
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Residues in contact with GLU 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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160A ASN* 5.1 6.1 - - - +
166A ARG* 5.0 1.7 + - - -
168A ASN* 4.3 7.4 + - - -
169A GLN* 4.3 15.9 + - - +
625B ASN 4.0 4.2 - - - +
626B GLU 3.7 19.9 - - - +
628B ILE* 1.3 93.0 + - + +
630B TYR* 1.3 87.6 + - + +
632B HIS* 3.9 6.4 - - - +
633B GLN* 2.9 26.4 + - - +
657B PHE* 4.2 14.6 - - + -
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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
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168A ASN* 3.2 32.0 + - - +
581B PHE* 4.0 8.5 - - + -
592B TRP* 4.1 10.3 - + + +
593B PRO* 4.5 10.2 - - + +
596B PHE* 3.5 64.4 - + + -
600B ILE* 4.0 9.0 - - + +
626B GLU 4.0 13.5 - - - -
627B ILE* 2.7 19.7 + - - +
629B GLU* 1.3 95.7 + - + +
631B ILE* 1.3 66.6 + - - +
632B HIS 3.2 1.3 - - - -
633B GLN* 3.1 32.6 + - - +
634B LEU* 3.7 8.7 - - - +
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Residues in contact with ILE 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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581B PHE* 3.3 26.7 - - + -
619B MET* 4.4 10.3 - - - -
624B PHE* 4.1 17.7 - - + -
627B ILE* 2.9 42.6 + - + +
628B ILE* 3.7 12.6 - - + +
630B TYR* 1.3 77.0 - - - +
632B HIS* 1.3 62.8 - - - +
634B LEU* 2.9 29.4 + - + +
636B PHE* 3.5 17.6 - - + -
639B ILE* 4.1 8.1 - - + -
654B PHE* 4.9 2.2 - - + -
660B TRP* 3.8 27.8 - - + -
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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
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628B ILE 3.0 16.2 + - - +
629B GLU 3.9 7.9 - - - +
630B TYR 3.2 0.4 - - - -
631B ILE* 1.3 81.2 - - - +
633B GLN* 1.3 62.0 + - + +
634B LEU 3.3 9.4 + - - +
636B PHE* 5.5 1.2 - - - -
657B PHE* 3.5 40.5 - + + -
659B GLY 4.3 14.8 - - - -
660B TRP* 4.2 19.5 - + + -
661B ILE* 5.7 1.8 - - + -
662B LYS* 4.4 15.7 + - + +
1203B SO4 4.7 5.0 + - - -
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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