Contacts of the helix formed by residues 637 - 644 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B PRO* 3.2 6.2 + - + +
635B CYS 3.2 1.2 - - - -
636B LEU* 1.3 78.7 - - - +
638B SER* 1.3 57.1 + - - +
640B PHE* 3.6 1.6 + - - +
641B SER* 3.0 47.1 + - - +
684B PHE* 3.8 29.3 - - + -
687B SER* 4.4 11.9 - - - -
688B LEU* 4.0 34.5 - - + +
691B ILE* 4.8 5.4 - - + -
737B ILE* 4.5 2.9 - - + -
738B SER* 4.3 15.3 - - - +
539C TYR* 5.3 2.2 - - - +
543C TYR* 2.9 36.8 - - + +
558C ARG* 5.8 1.3 - - - +
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Residues in contact with SER 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B CYS 4.3 1.7 + - - -
637B LEU* 1.3 77.6 - - - +
639B PRO* 1.3 74.3 - - - +
641B SER* 3.2 14.7 + - - -
642B LEU* 3.4 17.9 + - - +
539C TYR* 6.4 0.4 - - - -
540C GLU* 2.8 30.9 + - - -
543C TYR* 3.8 26.8 - - - -
544C LEU* 5.5 5.2 - - - -
558C ARG* 4.6 5.0 + - - +
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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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598B ALA* 3.4 24.9 - - + +
601B LEU* 3.9 29.3 - - + +
602B PRO* 4.6 6.5 - - + -
635B CYS 3.6 11.2 - - - +
636B LEU 3.2 15.3 - - - +
638B SER* 1.3 97.9 - - - +
640B PHE* 1.3 60.2 + - - +
642B LEU* 3.7 8.6 + - + +
643B LEU* 3.5 19.4 + - - +
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Residues in contact with PHE 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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588B MET* 5.7 0.2 - - + -
601B LEU* 3.7 30.3 - - + -
609B ALA 4.6 1.1 - - - -
612B ILE* 4.5 5.2 - - + -
613B LEU* 3.6 52.3 - - + -
616B THR* 4.1 17.9 - - + -
636B LEU* 3.1 50.6 + - + +
637B LEU* 3.9 4.5 - - + +
639B PRO* 1.3 77.3 - - - +
641B SER* 1.3 59.9 + - - +
643B LEU* 3.3 11.3 + - + +
644B LEU* 2.9 34.8 + - - +
684B PHE* 4.2 15.9 - + - -
688B LEU* 4.3 15.9 - - + -
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Residues in contact with SER 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 3.0 33.4 + - - +
638B SER 3.2 3.3 + - - -
640B PHE* 1.3 74.0 - - - +
642B LEU* 1.3 66.6 + - - +
644B LEU* 3.0 18.9 + - - +
645B TYR* 3.0 26.2 + - - -
691B ILE* 3.6 23.9 - - - +
556C ASP* 4.8 0.5 + - - -
558C ARG* 3.2 27.2 + - - -
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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
----------------------------------------------------------
638B SER* 3.4 12.4 + - - +
639B PRO* 4.1 9.6 - - + +
641B SER* 1.3 77.3 - - - +
643B LEU* 1.3 63.9 + - - +
645B TYR* 3.2 12.3 + - + +
646B HIS* 3.0 30.7 + - + +
540C GLU* 4.6 5.8 - - - +
558C ARG* 4.2 20.4 - - - +
562C ILE* 4.4 17.5 - - + -
602C PRO* 4.0 20.9 - - + +
603C PHE* 4.0 32.5 - - + +
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Residues in contact with LEU 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B THR* 3.9 29.4 - - + +
609B ALA* 3.8 29.6 - - + +
610B ALA* 3.9 22.9 - - - +
613B LEU* 4.0 23.8 - - + -
639B PRO 3.5 11.3 + - - +
640B PHE* 3.3 13.6 + - + +
641B SER 3.2 0.2 - - - -
642B LEU* 1.3 79.3 - - - +
644B LEU* 1.3 62.4 + - - +
646B HIS* 3.0 18.4 + - + +
647B LEU* 3.3 28.3 + - + +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LEU* 3.6 21.1 - - + -
640B PHE 2.9 25.5 + - - +
641B SER* 3.0 8.2 + - - +
643B LEU* 1.3 74.8 - - - +
645B TYR* 1.3 57.4 + - - +
646B HIS 3.1 2.8 + - - -
647B LEU* 3.9 4.7 + - + -
652B ILE* 3.7 18.0 - - + +
655B LEU* 4.1 5.8 - - + -
688B LEU* 3.9 26.7 - - + -
691B ILE* 3.3 33.0 - - + -
692B LEU* 3.4 34.1 - - + -
695B ARG* 3.0 29.1 + - + +
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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