Contacts of the helix formed by residues 93 - 102 (chain B) in PDB entry 4DVQ
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 LEU 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.7 28.7 - - + -
92B MET* 1.3 95.9 - - - +
94B PRO* 1.3 76.4 - - + +
95B GLU* 3.9 18.4 - - + +
96B ASP* 2.9 27.6 + - - +
97B VAL* 3.2 14.9 + - - +
393B GLN* 3.7 23.1 - - - +
405B VAL* 4.8 0.8 - - - +
410B LEU* 4.5 1.1 - - - -
413B ASN* 3.4 29.6 - - - +
416B LEU* 4.7 2.5 - - + -
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Residues in contact with PRO 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 1.3 83.5 - - + +
95B GLU* 1.3 64.8 + - - +
97B VAL* 3.0 9.6 + - + +
98B GLU* 2.9 24.8 + - - +
410B LEU* 3.4 16.4 - - + -
416B LEU* 3.2 36.3 - - + -
417B PHE* 5.8 0.2 - - + -
438B PHE* 3.5 38.5 - - + +
439B HIS* 4.1 20.2 - - + +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.9 19.0 - - + +
94B PRO* 1.3 79.3 - - - +
96B ASP* 1.3 63.6 + - - +
98B GLU* 3.4 12.2 + - - +
99B LYS* 3.2 44.3 + - - +
393B GLN* 3.3 26.6 + - - +
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO 4.3 1.6 - - - +
91B VAL* 3.2 44.5 - - + +
92B MET 4.2 0.5 + - - -
93B LEU* 2.9 32.2 + - - +
95B GLU* 1.3 73.4 - - - +
97B VAL* 1.3 64.6 + - - +
99B LYS* 3.4 2.3 + - - +
100B LEU* 3.0 23.0 + - - +
392B LEU* 3.6 34.6 - - + +
393B GLN* 3.0 29.3 + - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU 3.6 9.2 - - - +
94B PRO* 3.0 10.9 + - + +
96B ASP* 1.3 76.2 - - - +
98B GLU* 1.3 58.6 + - - +
100B LEU* 3.0 11.7 + - - +
101B GLN* 2.9 27.0 + - - +
382B LEU* 4.6 2.7 - - + -
405B VAL* 3.5 34.3 - - + -
410B LEU* 4.9 2.0 - - + -
438B PHE* 4.0 17.9 - - + -
441B VAL* 4.5 20.9 - - + -
445B PHE* 3.6 31.8 - - + -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO 2.9 12.0 + - - +
95B GLU* 3.5 15.7 - - - +
97B VAL* 1.3 74.0 - - - +
99B LYS* 1.3 69.3 + - + +
101B GLN* 3.2 12.5 + - - +
102B GLN* 3.3 29.3 + - - +
438B PHE* 3.5 44.8 - - + -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLU* 3.2 36.6 + - - +
96B ASP* 3.7 5.4 - - - +
98B GLU* 1.3 79.3 - - + +
100B LEU* 1.3 58.3 + - - +
102B GLN* 2.8 41.5 + - - +
103B VAL* 3.4 8.1 + - - +
390B LEU* 5.4 7.2 - - + +
391B VAL* 3.4 27.0 + - - +
392B LEU* 3.8 19.2 - - + +
393B GLN 5.7 2.6 - - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 5.9 0.2 - - + -
96B ASP 3.0 14.2 + - - +
97B VAL* 3.0 14.0 + - - +
99B LYS* 1.3 77.7 - - - +
101B GLN* 1.3 60.1 + - - +
103B VAL* 3.1 15.9 + - + +
104B ASP* 3.2 13.2 + - - +
382B LEU* 6.1 0.7 - - + -
383B GLU 5.7 0.4 - - - -
384B ARG* 3.9 17.4 - - + +
386B VAL* 3.6 31.2 - - + -
390B LEU* 4.2 13.5 - - + -
392B LEU* 5.0 1.3 - - + +
403B VAL* 4.0 31.2 - - + +
405B VAL* 4.2 19.3 - - + -
445B PHE* 3.9 22.7 - - + -
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL 2.9 10.8 + - - +
98B GLU 3.2 8.5 + - - +
100B LEU* 1.3 76.1 - - - +
102B GLN* 1.3 59.7 + - + +
103B VAL 3.1 4.3 + - - -
104B ASP* 3.4 21.0 + - - +
438B PHE* 3.2 31.3 - - + -
445B PHE* 3.7 29.3 - - + +
446B GLY* 3.7 26.3 + - - +
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 3.3 31.8 + - - +
99B LYS* 2.8 21.8 + - - +
101B GLN* 1.3 76.0 - - + +
103B VAL* 1.3 64.0 + - + +
104B ASP 3.7 2.3 - - - +
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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
------------------------------------------------------------
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