Contacts of the helix formed by residues 649 - 659 (chain C) 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 SER 649 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648C PRO* 1.3 74.7 - - - +
650C VAL* 1.3 55.2 + - - +
652C ILE* 4.0 3.3 - - - +
653C THR* 2.6 42.9 + - - -
699C LEU* 3.6 28.1 - - - +
700C GLN* 4.0 16.9 + - - -
710C GLN* 3.8 20.6 + - - +
714C TRP* 5.2 6.1 - - - +
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Residues in contact with VAL 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648C PRO* 3.9 18.2 - - + -
649C SER* 1.3 76.3 - - - +
651C SER* 1.3 67.1 + - - +
653C THR* 3.5 5.0 + - - -
654C SER* 3.0 31.0 + - - -
710C GLN* 3.7 28.0 - - + +
713C GLN* 5.7 0.2 - - - +
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Residues in contact with SER 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C MET* 5.6 0.2 - - - +
647C LEU* 4.1 19.4 - - - +
648C PRO* 3.3 26.2 + - - +
650C VAL* 1.3 83.0 - - - +
652C ILE* 1.3 60.2 + - - +
654C SER* 3.3 7.4 + - - -
655C LEU* 3.0 33.7 + - - +
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Residues in contact with ILE 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C LEU* 3.8 21.8 - - + +
647C LEU* 4.1 13.7 - - + +
648C PRO 3.2 16.6 + - - +
649C SER* 4.1 5.4 - - - +
651C SER* 1.3 77.2 - - - +
653C THR* 1.3 61.2 + - - +
655C LEU* 3.5 6.7 - - + +
656C LEU* 3.3 20.6 + - - +
692C LEU* 3.8 35.8 - - + +
695C ARG* 3.4 29.8 - - + -
696C GLY* 4.4 6.5 - - - +
699C LEU* 4.5 3.1 - - + -
714C TRP* 3.6 25.4 - - + -
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Residues in contact with THR 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649C SER* 2.6 26.6 + - - -
650C VAL* 3.8 6.5 - - - -
652C ILE* 1.3 74.7 - - - +
654C SER* 1.3 66.6 + - - +
656C LEU* 3.1 3.7 + - - +
657C ARG* 2.8 26.0 + - + +
710C GLN 5.7 0.4 + - - +
713C GLN* 3.4 43.3 - - + +
714C TRP* 3.7 37.9 - - + +
717C VAL* 4.8 2.7 - - + -
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Residues in contact with SER 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C MET* 4.5 12.6 - - - -
650C VAL 3.0 19.1 + - - -
651C SER* 3.6 7.2 - - - -
653C THR* 1.3 76.1 - - - +
655C LEU* 1.3 58.2 + - - +
657C ARG* 3.2 31.4 + - - +
658C GLN* 2.8 37.0 + - - +
713C GLN* 5.3 0.3 + - - -
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Residues in contact with LEU 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C LEU* 3.5 25.8 - - + +
614C MET* 3.8 39.5 - - + +
617C ALA* 4.4 8.1 - - + +
644C LEU* 3.5 32.1 - - + -
647C LEU* 4.4 10.5 - - + -
651C SER 3.0 15.8 + - - +
652C ILE* 3.5 11.2 - - + +
653C THR 3.1 0.2 - - - -
654C SER* 1.3 76.5 - - - +
656C LEU* 1.3 57.0 + - - +
658C GLN* 3.2 5.4 + - - +
659C LEU* 2.8 30.2 + - - +
692C LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652C ILE 3.3 7.3 + - - +
653C THR 3.1 7.0 + - - +
655C LEU* 1.3 73.8 - - - +
657C ARG* 1.3 68.7 + - - +
658C GLN 2.9 2.4 + - - -
659C LEU* 3.2 6.4 + - + +
660C MET* 3.1 39.5 + - + +
689C LEU* 3.6 30.5 - - + -
692C LEU* 4.0 21.1 - - + -
693C LEU* 3.6 22.7 - - + -
714C TRP* 3.5 31.2 - - + -
717C VAL* 3.7 26.5 - - + +
718C MET* 4.4 1.3 - - + -
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Residues in contact with ARG 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653C THR* 2.8 14.5 + - + +
654C SER* 3.3 30.6 + - - +
656C LEU* 1.3 75.2 - - - +
658C GLN* 1.3 75.4 + - - +
660C MET* 5.2 0.2 - - - -
661C ASN 3.0 2.1 + - - -
662C LEU* 2.7 50.0 + - + -
663C PRO* 3.3 18.4 - - + +
713C GLN* 3.3 34.7 + - + +
717C VAL* 4.1 20.7 - - + +
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Residues in contact with GLN 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C MET* 3.4 34.9 - - + +
617C ALA* 4.6 13.7 - - + +
618C ARG* 3.0 36.9 - - + +
654C SER* 2.8 21.6 + - - +
655C LEU* 3.3 9.4 - - - +
657C ARG* 1.3 95.3 - - - +
659C LEU* 1.3 60.9 + - - +
661C ASN* 2.4 33.6 + - - +
663C PRO* 4.4 14.4 - - - +
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Residues in contact with LEU 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C ALA* 4.1 24.8 - - + +
618C ARG 5.7 0.3 - - - +
620C LEU* 3.7 30.5 - - + -
621C PRO* 5.6 5.0 - - + +
655C LEU 2.8 18.5 + - - +
656C LEU* 3.7 8.5 - - + +
658C GLN* 1.3 74.4 - - - +
660C MET* 1.3 60.3 - - + +
661C ASN* 3.1 2.6 + - - +
675C HIS* 3.8 12.1 - - - +
676C LEU* 4.4 11.8 - - + +
679C VAL* 4.1 18.6 - - + +
685C GLY 5.5 0.4 - - - +
688C LEU* 5.4 5.4 - - + -
689C LEU* 3.9 31.9 - - + +
692C LEU* 3.8 26.2 - - + -
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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