Contacts of the helix formed by residues 941 - 946 (chain A) in PDB entry 2IVF
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 LYS 941 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A TYR* 3.2 37.9 - - + +
453A HIS* 2.9 26.6 + - - +
455A ASP* 2.8 34.1 + - - +
456A LEU* 4.0 2.6 - - - +
570A LEU* 5.7 1.3 - - + -
826A GLU* 2.9 35.3 + - - -
939A MET 3.7 2.4 + - - -
940A PRO* 1.3 70.1 - - - +
942A PRO* 1.3 71.6 - - + +
943A LEU* 3.9 19.3 - - + +
944A HIS* 3.0 36.4 + - + +
961A PRO* 3.7 8.5 - - - +
962A ALA 4.5 3.4 + - - +
965A THR* 4.7 2.6 - - + +
1980A GOL 3.9 6.3 + - - +
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Residues in contact with PRO 942 (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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452A TYR* 3.3 19.5 - - - +
566A THR* 4.7 3.6 - - + -
570A LEU* 3.5 22.9 - - + -
573A SER 4.7 0.2 - - - -
574A PHE* 3.9 36.1 - - + +
577A TYR* 3.5 26.9 - - + -
820A TRP* 3.5 7.5 - - - -
940A PRO 3.2 10.8 - - - +
941A LYS* 1.3 84.4 - - + +
943A LEU* 1.3 56.1 + - - +
944A HIS 3.0 0.7 - - - -
945A LEU* 3.0 29.6 + - + +
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Residues in contact with LEU 943 (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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570A LEU* 4.0 21.8 - - + -
577A TYR* 4.4 7.9 - - + +
820A TRP* 3.9 41.3 - - + +
821A TYR* 3.7 25.9 + - + +
824A ALA* 3.8 10.8 - - + -
826A GLU* 3.4 39.9 - - + +
941A LYS* 3.1 11.0 + - + +
942A PRO* 1.3 76.6 - - - +
944A HIS* 1.3 63.2 - - + +
945A LEU 3.1 0.7 - - - -
946A ALA* 3.0 22.7 + - - +
1981A GOL 3.1 11.6 + - - -
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Residues in contact with HIS 944 (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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226A MET* 3.5 35.8 - - + +
230A HIS* 3.9 9.6 - + - -
455A ASP* 2.8 24.8 + - - +
587A TRP* 3.8 0.3 - - - -
821A TYR* 3.7 12.6 - - - -
941A LYS* 3.0 26.5 + - + +
943A LEU* 1.3 82.6 - - + +
945A LEU* 1.3 55.9 + - - +
946A ALA 3.2 3.8 - - - -
960A SER* 3.7 2.9 + - - -
961A PRO* 3.6 29.1 - - + +
962A ALA 5.2 1.2 + - - -
1980A GOL 3.6 34.7 - - - -
1981A GOL 3.0 27.8 + - - -
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Residues in contact with LEU 945 (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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548A MET* 4.1 7.6 - - + -
574A PHE* 3.5 46.2 - - + +
577A TYR* 3.9 3.1 - - + -
578A LEU* 3.5 33.2 - - + +
581A ALA* 3.7 10.9 - - + +
586A TRP* 3.9 0.9 - - - +
587A TRP* 2.9 38.3 + - - +
820A TRP* 3.8 11.4 - - + -
942A PRO 3.0 17.7 + - - +
944A HIS* 1.3 75.5 - - - +
946A ALA* 1.3 64.3 + - - +
947A GLY 3.5 1.2 + - - -
961A PRO* 3.5 27.1 - - + -
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Residues in contact with ALA 946 (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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586A TRP* 4.0 2.5 - - - -
818A HIS* 3.9 11.7 - - + -
820A TRP* 3.5 22.0 - - + -
821A TYR* 4.3 3.1 - - + -
943A LEU 3.0 18.1 + - - +
944A HIS 3.2 1.0 - - - -
945A LEU* 1.3 79.4 - - - +
947A GLY* 1.3 57.6 + - - +
952A PHE* 3.5 18.5 - - + +
1981A GOL 2.9 34.9 - - - +
1982A GOL 3.1 3.7 - - - -
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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