Contacts of the helix formed by residues 959 - 966 (chain B) in PDB entry 2IVS
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 ARG 959 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798A GLY 5.8 2.5 - - - +
955B ILE* 4.4 7.2 - - + -
956B PRO* 2.7 35.3 + - + +
958B GLU* 1.3 74.4 - - + +
960B LEU* 1.3 60.3 + - - -
961B PHE 3.5 1.1 - - - -
962B ASN* 3.9 7.7 + - - +
963B LEU* 3.3 26.9 + - + +
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Residues in contact with LEU 960 (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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915B VAL* 4.1 11.9 - - + +
916B LYS* 3.8 42.2 - - + -
923B LEU* 5.4 0.2 - - + -
952B TYR* 3.6 43.1 - - + -
955B ILE* 4.8 8.3 - - + -
956B PRO 3.5 2.5 + - - +
957B PRO* 3.0 17.1 + - + +
959B ARG* 1.3 74.3 - - - +
961B PHE* 1.3 67.6 + - - +
962B ASN 3.2 2.0 - - - -
963B LEU* 3.1 11.8 + - + +
964B LEU* 2.9 46.9 + - + +
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Residues in contact with PHE 961 (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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766A PRO* 5.0 9.4 - - + -
769A LEU* 4.0 28.3 - - + -
915B VAL* 4.1 18.4 - - + -
923B LEU* 3.9 52.4 - - + +
924B PHE* 3.5 37.2 - + + -
957B PRO 3.8 18.8 - - - -
958B GLU 3.8 12.1 - - - +
959B ARG 3.5 0.2 - - - -
960B LEU* 1.3 78.4 - - - +
962B ASN* 1.3 61.7 + - + +
964B LEU* 3.3 1.6 + - - +
965B LYS 3.1 17.5 + - - -
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Residues in contact with ASN 962 (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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924B PHE* 5.0 1.3 - - - -
958B GLU 5.5 0.2 + - - -
959B ARG* 3.9 8.9 + - - +
960B LEU 3.2 0.4 - - - -
961B PHE* 1.3 78.8 - - + +
963B LEU* 1.3 66.8 + - + +
965B LYS* 3.5 6.3 + - - +
966B THR* 3.1 29.6 + - + +
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Residues in contact with LEU 963 (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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955B ILE* 3.8 34.3 - - + -
959B ARG* 3.3 19.1 - - + +
960B LEU* 3.1 14.7 + - + +
962B ASN* 1.3 82.1 - - + +
964B LEU* 1.3 60.1 + - + +
966B THR* 3.1 5.1 + - - +
968B HIS* 2.9 60.4 + - + +
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Residues in contact with LEU 964 (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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918B MET 4.5 3.1 - - - +
920B ILE* 3.8 19.2 - - + +
923B LEU* 3.7 30.1 - - + -
935B TRP* 3.8 28.3 - - + -
952B TYR* 3.7 23.8 - - + +
960B LEU* 2.9 40.3 + - + +
961B PHE 3.8 2.5 - - - +
963B LEU* 1.3 74.1 - - - +
965B LYS* 1.3 59.8 + - - +
967B GLY* 2.8 17.7 + - - -
968B HIS 3.6 15.9 - - - +
969B ARG* 3.0 21.9 + - - +
990B GLN* 5.4 0.7 + - - -
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Residues in contact with LYS 965 (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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920B ILE* 3.7 15.2 - - + +
924B PHE* 4.1 17.7 - - + -
961B PHE 3.1 16.7 + - - +
962B ASN* 3.5 6.5 + - - +
963B LEU 3.4 0.2 - - - -
964B LEU* 1.3 76.9 - - - +
966B THR* 1.3 62.7 + - + +
967B GLY* 3.1 1.3 + - - -
990B GLN* 4.4 12.7 + - - +
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Residues in contact with THR 966 (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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962B ASN* 3.1 19.2 + - + +
963B LEU* 3.8 2.3 - - - +
964B LEU 3.2 0.2 - - - -
965B LYS* 1.3 79.0 - - + +
967B GLY* 1.3 58.4 + - - +
968B HIS* 2.9 36.2 + - - -
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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