Contacts of the helix formed by residues 649 - 660 (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 SER 649 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648B PRO* 1.3 72.8 - - - +
650B VAL* 1.3 59.8 + - - +
652B ILE* 3.1 9.7 + - - +
653B THR* 2.9 33.2 + - - -
695B ARG* 5.2 1.7 - - - +
699B LEU* 4.5 10.0 - - - +
711B ASN* 4.4 11.0 + - - -
714B TRP* 2.9 33.1 + - - +
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Residues in contact with VAL 650 (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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648B PRO* 4.0 21.5 - - + -
649B SER* 1.3 74.4 - - - +
651B SER* 1.3 65.4 - - - +
653B THR* 3.4 7.3 + - - -
654B SER* 3.1 27.3 + - - -
711B ASN* 5.9 5.2 - - - +
713B GLN* 5.8 6.3 - - - +
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Residues in contact with SER 651 (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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610B ALA* 6.0 2.7 - - - -
647B LEU* 4.0 25.8 - - - +
648B PRO* 3.3 24.2 + - - +
649B SER 3.2 0.4 - - - -
650B VAL* 1.3 78.8 - - - +
652B ILE* 1.3 64.9 + - - +
654B SER* 3.5 5.2 + - - +
655B LEU* 3.1 33.9 + - - +
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Residues in contact with ILE 652 (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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644B LEU* 3.7 30.3 - - + +
647B LEU* 3.7 23.8 - - + +
648B PRO 3.3 15.3 - - - +
649B SER* 3.1 8.2 + - - +
651B SER* 1.3 76.3 - - - +
653B THR* 1.3 57.9 + - - +
655B LEU* 3.6 1.4 + - + +
656B LEU* 3.1 28.2 + - + +
692B LEU* 3.7 39.0 - - + +
695B ARG* 3.8 14.1 - - + +
714B TRP* 3.4 29.4 - - + -
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Residues in contact with THR 653 (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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649B SER* 2.9 18.9 + - - -
650B VAL* 3.7 8.4 - - - -
651B SER 3.2 0.2 - - - -
652B ILE* 1.3 75.1 - - - +
654B SER* 1.3 65.1 + - - +
656B LEU* 3.4 8.6 + - - +
657B ARG* 3.1 55.4 + - - +
711B ASN* 4.8 3.1 + - - -
713B GLN* 3.5 32.6 + - + +
714B TRP* 3.7 19.9 + - - -
717B VAL* 4.7 9.4 - - + -
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Residues in contact with SER 654 (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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614B MET* 4.7 11.2 - - - -
650B VAL 3.1 15.9 + - - -
651B SER* 3.9 6.1 - - - -
652B ILE 3.4 0.2 - - - -
653B THR* 1.3 78.0 - - - +
655B LEU* 1.3 57.9 + - - +
657B ARG* 3.4 22.2 + - - +
658B GLN* 3.0 32.7 + - - +
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Residues in contact with LEU 655 (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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610B ALA* 4.5 4.3 - - + +
613B LEU* 4.0 17.7 - - + +
614B MET* 3.5 47.3 - - + +
617B ALA* 4.6 6.4 - - + +
644B LEU* 4.1 16.8 - - + -
647B LEU* 3.8 27.4 - - + -
651B SER* 3.1 25.1 + - - +
652B ILE* 3.9 3.8 - - - +
654B SER* 1.3 75.0 - - - +
656B LEU* 1.3 59.0 + - - +
658B GLN* 3.2 4.5 + - - +
659B LEU* 2.8 32.4 + - - +
692B LEU* 4.0 15.2 - - + +
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Residues in contact with LEU 656 (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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652B ILE* 3.1 23.6 + - + +
653B THR* 3.7 5.4 - - - +
654B SER 3.3 0.2 - - - -
655B LEU* 1.3 76.7 - - - +
657B ARG* 1.3 57.8 + - - +
659B LEU* 4.1 1.3 - - - +
660B MET* 3.0 39.9 + - + +
689B LEU* 3.6 26.2 - - + -
692B LEU* 3.3 34.1 - - + +
693B LEU* 3.8 15.5 - - + -
714B TRP* 3.2 42.8 - - + -
717B VAL* 4.3 17.0 - - + -
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Residues in contact with ARG 657 (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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653B THR* 3.1 37.7 + - - +
654B SER* 3.8 21.1 + - - +
656B LEU* 1.3 75.5 - - - +
658B GLN* 1.3 61.2 + - + +
660B MET* 4.8 2.2 - - - -
661B ASN* 3.1 27.9 + - - +
713B GLN* 3.2 29.9 + - - -
716B GLU* 6.4 0.2 - - - -
717B VAL* 3.7 20.9 - - + -
720B MET* 5.9 5.4 - - + -
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Residues in contact with GLN 658 (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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614B MET* 3.7 28.6 - - + +
617B ALA* 3.8 6.6 - - + +
618B ARG* 3.2 49.3 - - - +
654B SER* 3.0 19.0 + - - +
655B LEU* 3.8 4.3 - - - +
657B ARG* 1.3 77.1 - - + +
659B LEU* 1.3 63.1 - - - +
661B ASN* 4.1 3.5 + - - +
675B HIS* 3.6 17.7 + - - -
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Residues in contact with LEU 659 (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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617B ALA* 4.0 22.2 - - + +
620B LEU* 3.5 33.0 - - + -
655B LEU 2.8 17.4 + - - +
656B LEU 4.1 2.2 - - - +
658B GLN* 1.3 76.7 - - - +
660B MET* 1.3 60.4 + - - +
675B HIS* 2.8 26.8 + - - -
679B VAL* 4.0 16.8 - - + +
685B GLY 4.6 1.8 - - - +
688B LEU* 4.1 9.9 - - + -
689B LEU* 3.6 46.7 - - + +
692B LEU* 3.7 17.9 - - + -
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Residues in contact with MET 660 (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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656B LEU* 3.0 31.2 + - - +
657B ARG* 4.6 1.3 - - - +
659B LEU* 1.3 75.6 - - + +
661B ASN* 1.3 76.4 - - - +
662B LEU 3.7 1.2 - - - +
663B PRO* 5.9 0.2 - - + -
676B LEU* 3.3 53.8 - - + +
679B VAL* 5.5 0.2 - - - -
689B LEU* 4.0 26.7 - - + -
693B LEU* 5.2 0.4 - - - -
717B VAL* 4.1 20.0 - - - +
720B MET* 4.0 23.3 - - + +
721B ALA* 3.6 37.5 - - + +
724B GLU* 5.1 1.1 - - + -
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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