Contacts of the helix formed by residues 93 - 103 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I PRO* 3.7 25.1 - - + -
91I VAL* 5.0 0.4 - - - +
92I MET* 1.3 90.6 - - - +
94I PRO* 1.4 73.8 - - + +
95I GLU* 4.3 16.4 - - + +
96I ASP* 3.1 31.6 + - - +
97I VAL* 3.5 10.6 + - - +
393I GLN* 3.6 29.6 - - - +
405I VAL* 5.2 0.8 - - - +
410I LEU* 4.5 2.2 - - - +
413I ASN* 3.5 28.0 - - - +
416I LEU* 4.4 2.0 - - + -
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Residues in contact with PRO 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I MET 4.4 2.5 - - - +
93I LEU* 1.4 85.8 - - + +
95I GLU* 1.3 58.4 + - + +
97I VAL* 2.9 28.1 + - + +
98I GLU* 3.3 10.8 + - - +
410I LEU* 4.5 16.3 - - + -
416I LEU* 3.2 36.3 - - + -
438I PHE* 3.7 28.7 - - + +
439I HIS* 3.5 26.5 - - + +
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Residues in contact with GLU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I LEU* 4.3 24.5 - - + +
94I PRO* 1.3 76.0 - - + +
96I ASP* 1.3 65.6 + - - +
98I GLU* 3.4 18.3 + - - +
99I LYS* 3.1 34.3 + - + +
393I GLN* 4.0 18.5 + - - +
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Residues in contact with ASP 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I PRO 4.4 3.1 - - - +
91I VAL* 3.5 41.0 - - + +
93I LEU* 3.1 31.0 + - - +
95I GLU* 1.3 81.4 - - - +
97I VAL* 1.3 56.1 + - - +
99I LYS* 3.5 5.4 + - - +
100I LEU* 2.9 29.5 + - - +
392I LEU* 3.8 20.6 - - + +
393I GLN* 3.3 36.3 + - - +
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Residues in contact with VAL 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I LEU 3.5 15.3 - - - +
94I PRO* 2.9 13.8 + - + +
96I ASP* 1.3 75.1 - - - +
98I GLU* 1.3 55.1 + - - +
100I LEU* 3.2 6.0 + - - +
101I GLN* 2.8 33.4 + - - +
382I LEU* 4.6 3.4 - - + -
405I VAL* 3.9 30.3 - - + -
410I LEU* 4.4 6.7 - - + -
438I PHE* 4.2 15.3 - - + +
441I VAL* 4.2 13.5 - - + -
445I PHE* 3.3 36.9 - - + -
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Residues in contact with GLU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I PRO 3.3 6.8 + - - +
95I GLU* 3.5 19.9 - - - +
97I VAL* 1.3 74.6 - - - +
99I LYS* 1.3 66.6 + - + +
101I GLN* 3.1 2.5 + - - +
102I GLN* 2.9 32.3 + - + +
438I PHE* 3.7 39.9 - - + +
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Residues in contact with LYS 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I GLU* 3.1 23.4 + - + +
96I ASP* 3.6 8.5 - - - +
98I GLU* 1.3 81.3 - - + +
100I LEU* 1.3 60.5 + - - +
102I GLN* 3.5 17.5 - - - +
103I VAL* 3.2 28.2 + - - +
390I LEU* 4.3 4.8 - - + +
391I VAL* 3.7 31.8 + - + +
392I LEU* 3.8 16.2 - - + -
393I GLN 6.0 0.9 - - - +
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Residues in contact with LEU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I VAL* 5.7 0.2 - - + -
96I ASP 2.9 17.2 + - - +
97I VAL* 3.5 7.2 - - - +
98I GLU 3.1 0.2 - - - -
99I LYS* 1.3 76.2 - - - +
101I GLN* 1.3 63.7 + - - +
103I VAL* 3.4 6.8 + - + -
104I ASP* 3.3 20.3 + - - +
382I LEU* 6.0 1.1 - - + +
384I ARG* 4.0 24.9 - - + -
386I VAL* 4.1 20.9 - - + -
390I LEU* 4.7 11.9 - - + -
392I LEU* 5.4 0.7 - - + -
403I VAL* 3.6 33.4 - - + +
405I VAL* 4.2 20.2 - - + -
445I PHE* 4.0 19.1 - - + -
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Residues in contact with GLN 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I VAL 2.8 20.0 + - - +
98I GLU* 3.1 5.1 + - - +
100I LEU* 1.3 69.6 - - - +
102I GLN* 1.3 67.3 + - - +
103I VAL 3.0 2.0 - - - -
104I ASP* 2.8 25.8 + - + +
438I PHE* 3.6 22.2 - - + -
445I PHE* 3.7 29.9 - - + +
446I GLY* 3.9 26.6 - - - +
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Residues in contact with GLN 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I GLU* 2.9 23.3 + - - +
99I LYS* 3.5 21.3 - - - +
101I GLN* 1.3 77.1 - - - +
103I VAL* 1.3 60.7 + - + +
104I ASP 3.6 5.0 + - - +
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Residues in contact with VAL 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I LYS 3.2 18.2 - - - +
100I LEU* 3.4 9.9 + - + +
101I GLN 3.0 1.0 - - - -
102I GLN* 1.3 78.1 - - + +
104I ASP* 1.3 67.1 + - - +
105I SER* 3.0 4.9 + - - -
386I VAL* 3.7 22.9 - - + -
387I SER* 4.3 7.8 + - - +
388I SER* 3.7 31.5 + - - +
389I ASP 4.6 3.4 - - - +
390I LEU* 4.0 21.8 - - + -
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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