Contacts of the helix formed by residues 97 - 109 (chain W) in PDB entry 2Q4G
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 THR 97 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69W ASP* 2.6 32.7 + - - +
95W CYS 4.1 8.3 - - - +
96W LEU* 1.3 80.4 - - - +
98W GLY* 1.3 65.9 + - - +
99W ALA* 2.9 18.1 + - - +
100W GLY* 3.0 11.4 + - - -
101W CYS* 3.6 10.0 + - - -
123W LEU* 3.3 16.4 - - + +
124W LEU* 4.2 4.7 - - - -
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Residues in contact with GLY 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97W THR* 1.3 76.3 - - - +
99W ALA* 1.3 56.0 + - - +
100W GLY 3.0 5.2 + - - -
101W CYS* 3.2 17.1 + - - +
102W GLY 4.4 2.4 + - - -
123W LEU 3.6 7.5 + - - -
124W LEU 3.6 18.2 + - - -
128W GLY* 3.9 17.5 - - - -
131W LEU* 4.9 4.3 - - - +
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Residues in contact with ALA 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69W ASP* 3.9 11.9 - - + +
97W THR* 2.9 14.3 + - - +
98W GLY* 1.3 76.2 - - - +
100W GLY* 1.3 56.4 + - - +
102W GLY 5.0 1.9 + - - -
103W VAL* 5.6 3.3 + - - +
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Residues in contact with GLY 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69W ASP* 3.6 22.6 + - - -
72W VAL* 5.9 0.7 - - - +
76W LEU* 5.5 0.5 - - - +
96W LEU* 4.0 13.4 - - - +
97W THR 3.0 7.6 + - - -
99W ALA* 1.3 78.4 - - - +
101W CYS* 1.3 65.6 + - - +
102W GLY 3.2 4.1 + - - -
103W VAL* 3.3 12.6 + - - +
104W LEU* 3.2 19.1 + - - +
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Residues in contact with CYS 101 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96W LEU* 5.4 2.7 - - - -
97W THR 3.6 6.0 + - - -
98W GLY* 3.2 10.5 + - - +
100W GLY* 1.3 74.9 - - - +
102W GLY* 1.3 61.5 - - - +
104W LEU* 3.8 9.5 - - - +
105W SER* 2.7 32.7 + - - -
124W LEU* 3.8 33.0 - - - -
128W GLY* 3.2 44.0 - - - +
129W LEU* 4.2 0.9 - - - -
131W LEU* 4.1 5.8 - - + -
132W LEU* 4.5 11.1 - - + +
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Residues in contact with GLY 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98W GLY 4.4 1.8 + - - -
99W ALA 5.0 1.6 + - - -
100W GLY* 3.2 1.4 - - - -
101W CYS* 1.3 76.6 - - - +
103W VAL* 1.3 63.6 + - - +
105W SER* 3.2 3.7 + - - -
106W SER* 2.9 25.7 + - - -
131W LEU* 3.6 26.3 - - - +
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Residues in contact with VAL 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72W VAL* 6.0 0.2 - - + -
73W HIS* 3.4 56.5 - - + +
76W LEU* 3.7 20.0 - - + -
99W ALA 5.6 2.4 + - - +
100W GLY* 3.3 14.2 + - - +
102W GLY* 1.3 75.5 - - - +
104W LEU* 1.3 52.7 + - - +
106W SER* 3.0 11.0 + - - +
107W THR* 2.4 39.4 + - - +
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Residues in contact with LEU 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72W VAL* 5.8 1.6 - - + -
76W LEU* 3.8 34.3 - - + +
89W LEU* 5.3 2.5 - - + -
91W LEU* 4.6 9.4 - - + -
96W LEU* 4.5 16.6 - - + -
100W GLY 3.2 10.4 + - - +
101W CYS* 3.8 11.4 - - - +
103W VAL* 1.3 76.7 - - - +
105W SER* 1.3 60.6 + - - +
107W THR* 2.8 4.1 + - + -
108W LEU* 2.8 49.7 + - + +
117W LEU* 4.5 7.9 - - + -
119W LEU* 4.1 29.2 - - + -
132W LEU* 3.5 22.9 - - + -
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Residues in contact with SER 105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101W CYS 2.7 24.6 + - - -
102W GLY* 3.4 7.6 - - - -
104W LEU* 1.3 74.1 - - - +
106W SER* 1.3 61.8 + - - +
107W THR 3.2 1.0 + - - -
108W LEU* 3.4 8.2 + - - +
109W ARG* 3.7 9.6 + - - +
131W LEU* 3.1 27.7 + - - +
132W LEU* 3.9 14.3 - - - +
134W GLU* 4.2 1.4 - - - +
135W GLY* 3.2 32.7 + - - -
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Residues in contact with SER 106 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102W GLY 2.9 14.7 + - - -
103W VAL* 3.0 15.6 + - - +
105W SER* 1.3 76.7 + - - +
107W THR* 1.3 61.2 + - - +
109W ARG* 4.1 17.4 + - - +
110W THR* 3.9 15.9 - - - +
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Residues in contact with THR 107 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76W LEU* 3.6 42.7 - - + +
79W LEU* 5.2 0.7 - - + -
80W GLN* 5.6 5.8 + - + +
103W VAL* 2.4 31.2 + - - +
104W LEU* 2.8 12.4 + - + -
106W SER* 1.3 77.7 + - - +
108W LEU* 1.3 60.0 + - + +
109W ARG 3.1 2.2 - - - -
110W THR* 2.8 30.9 + - - +
111W LEU* 3.6 25.8 - - + +
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Residues in contact with LEU 108 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89W LEU* 6.0 0.4 - - + -
104W LEU* 2.8 23.5 + - + +
105W SER* 3.4 6.2 + - - +
107W THR* 1.3 77.0 - - + +
109W ARG* 1.3 58.6 + - - +
110W THR 3.1 2.6 + - - -
111W LEU* 3.7 16.1 + - + +
114W LEU* 3.6 30.3 - - + -
117W LEU* 4.2 19.1 - - + -
132W LEU* 3.4 29.2 - - + -
135W GLY 4.7 6.5 - - - +
136W LEU* 3.3 35.0 - - + +
140W GLN 4.4 0.9 - - - +
141W CYS* 4.0 23.2 - - - -
143W LEU* 4.9 4.5 - - + -
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Residues in contact with ARG 109 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105W SER* 3.7 16.0 + - - +
106W SER* 4.2 15.5 - - - +
107W THR 3.1 0.8 - - - -
108W LEU* 1.3 75.5 - - - +
110W THR* 1.3 63.8 + - + +
111W LEU 3.7 0.4 - - - -
134W GLU* 3.4 36.5 + - - +
135W GLY* 3.9 7.9 - - - +
138W ASP* 2.6 62.2 + - + +
140W GLN* 3.2 29.4 + - - +
141W CYS 5.0 0.2 - - - +
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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