Contacts of the helix formed by residues 100 - 111 (chain B) in PDB entry 4XQ2
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 TYR 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TYR* 5.2 2.6 - - - -
48A ARG* 3.1 22.7 + - - -
77B GLN* 3.4 17.3 - - - -
99B VAL* 1.3 77.7 - - - +
101B ALA* 1.3 65.0 + - + +
102B GLY* 3.3 19.4 - - - -
103B THR* 3.1 21.9 + - - +
104B ASP* 2.8 31.4 + - - +
143B GLU* 3.5 23.8 + - - +
147B ASN* 5.6 9.6 - - - +
197B LLP 3.4 47.3 + + + +
338B THR* 6.3 4.3 - - + -
339B HIS* 6.4 0.2 - - - -
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Residues in contact with ALA 101 (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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99B VAL 3.6 1.9 + - - -
100B TYR* 1.3 84.6 - - + +
102B GLY* 1.3 61.9 + - - +
104B ASP* 3.3 8.1 + - - +
105B GLY* 3.1 18.0 + - - -
338B THR 4.7 13.9 - - - +
339B HIS* 6.1 2.6 + - + -
341B PRO* 5.6 10.8 - - + -
342B LEU* 6.0 9.0 - - + -
350B ARG* 6.0 2.2 - - - +
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Residues in contact with GLY 102 (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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48A ARG* 5.6 2.7 - - - -
227A THR* 4.5 1.5 - - - +
77B GLN* 3.1 36.4 + - - -
100B TYR* 3.3 16.7 - - - -
101B ALA* 1.3 74.1 - - - +
103B THR* 1.3 65.6 + - - +
105B GLY* 3.1 11.8 + - - -
106B LEU* 3.2 8.3 + - - +
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Residues in contact with THR 103 (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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77B GLN* 3.3 5.8 + - - -
80B ALA* 5.6 2.5 - - + +
84B LEU* 5.5 1.1 - - + -
99B VAL* 4.0 7.0 - - + -
100B TYR* 3.1 36.0 + - - +
102B GLY* 1.3 75.2 - - - +
104B ASP* 1.3 61.5 + - - +
106B LEU* 3.0 21.0 + - - +
107B PHE* 3.1 25.7 + - + -
141B TRP* 3.5 42.8 - - + +
143B GLU* 4.2 4.0 + - - -
172B ASP* 4.3 6.8 + - - -
197B LLP 4.5 1.4 + - - -
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Residues in contact with ASP 104 (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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97B ASP 5.5 2.6 - - - +
99B VAL* 4.3 9.6 - - + +
100B TYR 2.8 17.4 + - - +
101B ALA* 3.7 9.4 - - - +
102B GLY 3.3 0.2 - - - -
103B THR* 1.3 74.8 - - - +
105B GLY* 1.3 56.7 + - - +
107B PHE* 3.2 13.6 + - - +
108B ASP* 2.9 35.0 + - - +
119B TYR* 2.2 36.3 + - - -
342B LEU* 5.9 3.1 - - - +
350B ARG* 6.0 4.5 - - - +
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Residues in contact with GLY 105 (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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227A THR* 3.9 13.9 - - - -
101B ALA 3.1 13.5 + - - -
102B GLY* 3.1 6.4 + - - -
104B ASP* 1.3 76.7 - - - +
106B LEU* 1.3 57.2 + - - +
108B ASP* 3.1 14.0 + - - +
109B LEU* 2.9 33.1 + - - +
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Residues in contact with LEU 106 (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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227A THR* 3.9 19.7 - - + +
228A ALA* 4.9 1.3 - - - -
77B GLN* 3.5 42.2 - - - +
80B ALA* 3.5 22.7 - - + -
81B ALA* 3.6 25.6 - - + +
84B LEU* 3.6 19.9 - - + +
102B GLY 3.2 6.6 + - - +
103B THR* 3.0 10.3 + - - +
105B GLY* 1.3 72.7 - - - +
107B PHE* 1.3 64.6 + - - +
109B LEU* 4.5 13.0 - - + +
110B ALA* 3.1 26.3 + - - +
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Residues in contact with PHE 107 (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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84B LEU* 4.5 10.1 - - + -
93B VAL* 4.1 18.6 - - + -
95B SER* 3.4 39.3 - - - -
99B VAL* 3.6 17.0 - - + -
103B THR* 3.1 25.7 + - + -
104B ASP* 3.2 17.2 + - - +
106B LEU* 1.3 79.7 - - - +
108B ASP* 1.3 53.9 + - - +
110B ALA* 3.2 6.1 + - + +
111B ALA* 2.8 35.6 + - - +
117B VAL* 4.0 23.8 - - + +
119B TYR* 3.3 30.5 - + - +
141B TRP* 4.1 16.2 - + + -
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Residues in contact with ASP 108 (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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104B ASP* 2.9 23.6 + - - +
105B GLY* 3.1 15.8 + - - +
107B PHE* 1.3 73.9 - - - +
109B LEU* 1.3 66.8 + - + +
111B ALA* 3.2 19.5 + - - +
112B ARG* 3.0 31.6 + - - +
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Residues in contact with LEU 109 (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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224A TYR* 4.2 28.5 - - + -
227A THR* 3.8 28.9 - - + +
228A ALA 5.4 0.7 - - - +
105B GLY 2.9 16.9 + - - +
106B LEU* 4.5 12.8 - - + +
108B ASP* 1.3 78.4 - - + +
110B ALA* 1.3 62.4 + - - +
112B ARG* 3.1 39.7 + - - +
113B GLN* 4.0 8.9 + - - +
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Residues in contact with ALA 110 (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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84B LEU* 5.3 12.8 - - + +
87B VAL* 6.3 0.2 - - + -
93B VAL* 5.9 1.8 - - + -
106B LEU 3.1 21.9 + - - +
107B PHE* 3.2 8.2 + - + +
109B LEU* 1.3 77.3 - - - +
111B ALA* 1.3 58.2 + - - +
112B ARG 3.0 0.2 - - - -
113B GLN* 2.9 24.6 + - - +
115B VAL* 3.1 42.1 + - + +
117B VAL* 5.2 0.4 - - + -
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Residues in contact with ALA 111 (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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107B PHE 2.8 12.8 + - - +
108B ASP* 3.3 17.5 - - - +
109B LEU 3.1 0.4 - - - -
110B ALA* 1.3 76.3 - - - +
112B ARG* 1.3 64.1 + - + +
113B GLN 3.6 0.7 + - - -
114B GLY* 4.0 7.1 + - - -
115B VAL 3.6 18.4 + - - +
117B VAL* 5.0 5.8 - - + -
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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