Contacts of the helix formed by residues 649 - 659 (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 SER 649 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648A PRO* 1.3 74.2 - - - +
650A VAL* 1.3 63.9 + - - +
652A ILE* 3.2 6.9 + - - +
653A THR* 3.1 23.7 + - - -
696A GLY* 6.1 0.8 - - - -
699A LEU* 3.4 22.7 - - - +
700A GLN* 2.3 35.2 + - - -
710A GLN* 3.0 11.6 + - - -
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Residues in contact with VAL 650 (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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648A PRO* 4.0 18.6 - - + -
649A SER* 1.3 76.0 - - - +
651A SER* 1.3 61.2 + - - +
653A THR* 3.3 3.3 + - - -
654A SER* 2.9 34.6 + - - +
710A GLN* 3.1 33.8 + - + +
713A GLN* 5.2 2.8 - - - +
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Residues in contact with SER 651 (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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610A ALA* 5.9 2.3 - - - +
647A LEU* 4.1 19.5 - - - +
648A PRO* 3.3 30.9 + - - +
649A SER 3.2 0.6 - - - -
650A VAL* 1.3 78.4 - - - +
652A ILE* 1.3 62.1 + - - +
654A SER* 3.2 7.9 + - - -
655A LEU* 2.9 35.9 + - - +
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Residues in contact with ILE 652 (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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644A LEU* 4.1 19.5 - - + +
647A LEU* 3.9 20.6 - - + -
648A PRO 3.3 15.5 + - - +
649A SER* 3.2 7.1 + - - +
651A SER* 1.3 75.1 - - - +
653A THR* 1.3 58.7 + - - +
655A LEU* 3.3 9.2 + - + +
656A LEU* 2.9 34.8 + - + +
692A LEU* 3.5 33.2 - - + +
695A ARG* 3.7 27.8 - - + -
696A GLY* 4.0 14.6 - - - +
699A LEU* 4.4 6.1 - - + -
714A TRP* 4.6 2.7 - - + -
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Residues in contact with THR 653 (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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649A SER* 3.1 8.5 + - - -
650A VAL 3.6 1.6 - - - -
652A ILE* 1.3 76.6 - - - +
654A SER* 1.3 54.1 + - - +
656A LEU* 3.3 4.4 + - - +
657A ARG* 2.7 41.0 + - + +
710A GLN* 3.0 31.7 + - - +
713A GLN* 3.6 46.4 - - + +
714A TRP* 3.5 26.2 - - - +
717A VAL* 4.4 5.6 - - + +
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Residues in contact with SER 654 (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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614A MET* 3.9 14.6 - - - +
650A VAL* 2.9 17.0 + - - +
651A SER* 3.2 11.3 + - - -
653A THR* 1.3 76.4 - - - +
655A LEU* 1.3 53.3 + - - +
657A ARG* 3.6 13.9 - - - +
658A GLN* 2.7 36.0 + - - +
713A GLN* 5.8 0.2 + - - -
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Residues in contact with LEU 655 (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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610A ALA* 4.4 3.4 - - + +
613A LEU* 3.6 36.3 - - + +
614A MET* 3.6 37.0 - - + +
617A ALA* 4.4 5.5 - - + +
647A LEU* 3.6 31.4 - - + -
651A SER* 2.9 21.2 + - - +
652A ILE* 3.5 10.3 - - + +
654A SER* 1.3 76.6 - - - +
656A LEU* 1.3 58.8 + - - +
658A GLN* 3.2 2.9 + - - +
659A LEU* 2.8 29.3 + - - +
692A LEU* 3.9 26.1 - - + +
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Residues in contact with LEU 656 (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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652A ILE* 2.9 15.9 + - + +
653A THR* 3.8 2.5 - - - +
655A LEU* 1.3 72.7 - - - +
657A ARG* 1.3 61.5 + - - +
659A LEU* 3.6 3.5 - - + +
660A MET* 2.9 38.8 + - + +
689A LEU* 3.5 30.3 - - + -
692A LEU* 3.5 33.0 - - + +
693A LEU* 3.5 36.3 - - + +
714A TRP* 3.6 27.4 - - + -
717A VAL* 3.4 17.3 - - + -
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Residues in contact with ARG 657 (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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653A THR* 2.7 22.1 + - - +
654A SER* 3.7 12.6 - - - +
656A LEU* 1.3 73.7 - - - +
658A GLN* 1.3 56.9 + - + +
660A MET 3.7 0.5 + - - -
661A ASN 3.3 1.6 + - - -
662A LEU* 2.8 55.7 + - + +
663A PRO* 3.6 35.2 - - + +
713A GLN* 4.0 41.2 + - - +
716A GLU* 3.2 25.4 + - - -
717A VAL* 4.1 16.6 - - + +
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Residues in contact with GLN 658 (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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614A MET* 3.3 44.5 - - + +
617A ALA* 4.1 7.4 - - + +
618A ARG* 3.2 44.4 + - - +
654A SER 2.7 18.4 + - - +
655A LEU 3.4 4.5 - - - +
657A ARG* 1.3 76.8 - - + +
659A LEU* 1.3 64.9 + - - +
661A ASN* 3.0 15.2 + - - +
662A LEU 4.3 9.2 + - - -
663A PRO* 5.7 1.6 - - - +
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Residues in contact with LEU 659 (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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617A ALA* 3.9 27.0 - - + +
620A LEU* 3.6 31.9 - - + -
621A PRO* 5.7 4.7 - - + +
655A LEU 2.8 20.2 + - - +
656A LEU* 3.2 5.6 + - + +
658A GLN* 1.3 74.7 - - - +
660A MET* 1.3 59.4 + - + +
661A ASN* 3.1 4.6 + - - +
675A HIS 4.4 5.4 - - - +
676A LEU* 5.2 1.9 - - + +
679A VAL* 4.1 23.7 - - + +
685A GLY 4.7 0.9 - - - +
688A LEU* 4.7 5.4 - - + -
689A LEU* 3.6 47.1 - - + +
692A LEU* 4.2 14.6 - - + -
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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