Contacts of the helix formed by residues 637 - 643 (chain A) in PDB entry 2XER
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 LEU 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A PRO* 3.4 14.8 + - + +
636A LEU* 1.3 78.9 - - - +
638A SER* 1.3 54.4 + - - +
640A PHE* 3.3 3.4 + - + +
641A SER* 2.7 39.2 + - - +
684A PHE* 3.6 19.1 - - + -
687A SER* 4.0 22.9 - - - +
688A LEU* 4.4 7.4 - - + +
691A ILE* 3.9 28.9 - - + -
737A ILE* 3.1 50.3 - - + -
738A SER* 4.5 7.9 - - - +
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Residues in contact with SER 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A PRO 4.7 1.0 + - - -
635A CYS 4.6 2.0 + - - -
637A LEU* 1.3 78.6 - - - +
639A PRO* 1.3 71.0 - - - +
641A SER* 3.1 23.0 + - - -
642A LEU* 3.3 20.2 + - - +
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Residues in contact with PRO 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ALA* 3.4 24.5 - - + +
601A LEU* 3.5 31.5 - - + +
602A PRO* 5.0 4.3 - - + -
635A CYS 3.4 15.0 - - - +
636A LEU* 3.1 16.8 - - - +
638A SER* 1.3 97.7 - - - +
640A PHE* 1.3 61.6 + - - +
642A LEU* 3.4 11.3 + - + +
643A LEU* 3.3 19.2 + - - +
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Residues in contact with PHE 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A VAL* 5.7 0.4 - - + -
601A LEU* 3.7 33.4 - - + -
609A ALA 4.6 0.2 - - - -
612A ILE* 4.5 4.9 - - + -
613A LEU* 3.6 56.1 - - + -
616A THR* 4.0 20.4 - - + -
636A LEU* 3.0 37.0 + - + +
637A LEU* 3.8 4.7 - - + +
639A PRO* 1.3 74.9 - - - +
641A SER* 1.3 66.0 - - - +
643A LEU* 3.2 11.7 + - + +
644A LEU* 3.1 29.0 + - + +
684A PHE* 3.7 27.8 - + - -
688A LEU* 4.9 10.1 - - + -
691A ILE* 5.7 0.2 - - - -
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Residues in contact with SER 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A LEU* 2.7 34.5 + - - +
638A SER* 3.1 13.0 + - - -
640A PHE* 1.3 75.5 - - - +
642A LEU* 1.3 65.0 + - - +
644A LEU* 3.2 14.9 + - - +
645A TYR* 3.3 25.3 - - - -
691A ILE* 4.3 24.2 - - - +
738A SER* 5.5 1.9 + - - -
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Residues in contact with LEU 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A PRO* 6.2 3.8 - - + -
638A SER* 3.3 23.6 + - - +
639A PRO* 3.8 8.7 - - + +
640A PHE 3.3 0.2 - - - -
641A SER* 1.3 77.0 - - - +
643A LEU* 1.3 63.7 + - - +
645A TYR* 3.2 24.5 + - + +
646A HIS* 3.0 24.0 + - - +
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Residues in contact with LEU 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A LEU* 5.2 1.3 - - + -
606A THR* 4.1 28.3 - - + +
609A ALA* 3.5 50.3 - - + +
610A ALA* 3.9 3.8 - - - +
613A LEU* 4.1 22.2 - - + -
639A PRO 3.3 10.5 + - - +
640A PHE* 3.2 18.1 + - + +
642A LEU* 1.3 79.5 - - - +
644A LEU* 1.3 63.4 + - + +
646A HIS* 3.1 19.9 + - + +
647A LEU* 3.4 16.9 - - + +
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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