Contacts of the helix formed by residues 102 - 116 (chain B) in PDB entry 2Q41
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 ASP 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B TYR* 5.1 1.7 - - + -
98B LEU* 5.5 0.2 - - - -
99B THR* 2.6 28.9 + - - +
101B ARG* 1.3 79.9 - - + +
103B GLU* 1.3 66.8 + - - +
104B CYS* 3.1 5.7 + - - +
105B ALA* 3.3 16.4 + - - +
106B TYR* 4.1 1.9 + - - +
267B VAL* 4.1 9.9 - - - +
268B PRO* 3.6 13.8 - - + +
269B THR* 2.4 45.3 + - - +
239C TRP* 3.8 26.2 - - + -
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Residues in contact with GLU 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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98B LEU* 2.8 29.8 - - + +
99B THR 3.1 28.1 + - - +
100B GLU* 3.8 20.7 + - - +
101B ARG 3.9 1.0 - - - -
102B ASP* 1.3 77.4 - - - +
104B CYS* 1.3 63.2 + - - +
105B ALA 3.2 0.7 + - - -
106B TYR* 3.4 5.8 + - - +
107B GLN* 2.9 47.1 + - - +
131B ASP* 2.8 26.3 - - - +
164B PHE* 5.2 0.2 - - - -
166B ASP* 4.7 0.5 - - - +
167B VAL* 3.2 25.6 - - + +
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Residues in contact with CYS 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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100B GLU 5.4 0.8 + - - -
101B ARG 4.8 3.6 - - - -
102B ASP* 3.1 6.7 - - - -
103B GLU* 1.3 79.1 - - - +
105B ALA* 1.3 65.3 + - - +
107B GLN* 4.4 4.7 + - - -
108B GLU* 2.6 57.0 + - - +
136B ARG* 4.8 9.4 - - - +
308B LYS* 4.2 34.3 - - + +
309B PHE* 4.4 5.8 - - - -
239C TRP* 4.3 21.1 - - - -
324C PHE* 5.6 2.0 - - - -
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Residues in contact with ALA 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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102B ASP 3.3 10.5 + - - +
103B GLU 3.2 0.8 + - - -
104B CYS* 1.3 82.1 - - - +
106B TYR* 1.3 65.0 + - - +
108B GLU* 3.8 0.2 - - - +
109B MSE 2.9 30.9 + - - +
265B THR* 5.0 0.2 - - - +
266B SER 3.3 25.8 - - - +
267B VAL* 4.3 6.7 - - + -
309B PHE* 3.9 20.0 - - + -
239C TRP* 4.1 17.0 - - + -
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Residues in contact with TYR 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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102B ASP 4.1 1.0 + - - +
103B GLU* 3.4 7.2 + - - +
105B ALA* 1.3 79.1 - - - +
107B GLN* 1.3 67.7 + - + +
109B MSE 3.9 0.6 - - - +
110B ILE* 2.8 57.5 + - + +
201B ASP* 2.9 41.1 + - - -
234B GLN* 3.3 32.3 + - + +
265B THR* 4.9 0.4 - - - -
267B VAL* 4.2 11.1 - - + +
270B TYR* 3.6 45.5 - + + +
275B ILE* 4.0 7.4 - - + -
277B PHE* 3.3 34.3 - + - -
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Residues in contact with GLN 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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98B LEU* 5.0 2.4 - - - +
103B GLU* 2.9 46.7 + - - +
104B CYS 4.1 1.3 - - - +
106B TYR* 1.3 84.3 - - + +
108B GLU* 1.3 63.1 + - - +
110B ILE* 3.8 6.5 - - - -
111B THR* 3.1 28.8 + - - -
131B ASP* 2.7 23.2 + - - -
133B GLY* 3.1 25.3 - - - -
134B VAL* 3.9 10.5 - - + +
136B ARG* 2.6 32.9 + - - +
137B GLU* 3.6 13.1 - - + +
167B VAL* 3.5 3.5 - - - +
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Residues in contact with GLU 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 CYS* 2.6 42.2 + - - +
105B ALA 3.8 1.3 - - - +
107B GLN* 1.3 73.7 - - - +
109B MSE 1.3 58.4 + - - +
112B HIS* 2.9 40.7 + - + +
136B ARG* 5.5 0.2 - - - +
137B GLU* 3.7 5.8 - - - +
307B LEU* 2.9 41.8 - - + +
308B LYS* 2.7 21.0 + - - +
309B PHE* 2.6 13.0 + - + -
310B TYR* 2.5 43.9 + - + +
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Residues in contact with MSE 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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105B ALA 2.9 17.4 + - - +
106B TYR 3.9 1.3 - - - +
108B GLU* 1.3 74.1 - - - +
110B ILE* 1.3 60.5 + - - +
113B LEU* 2.9 50.0 + - + +
265B THR* 3.3 30.1 - - - +
277B PHE* 3.9 17.0 - - + -
309B PHE* 3.8 9.2 - - + -
310B TYR* 3.6 27.4 - - + -
314B ILE* 3.6 31.2 - - + +
315B HIS* 4.9 0.2 - - - -
318B ALA* 3.6 29.2 - - + -
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Residues in contact with ILE 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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106B TYR* 2.8 63.3 + - + +
107B GLN* 3.3 13.9 - - - +
109B MSE 1.3 74.1 - - - +
111B THR* 1.3 67.9 + - - +
114B PRO* 3.0 22.0 - - - +
134B VAL* 4.0 13.5 - - + -
199B ILE* 3.9 23.6 - - + +
200B VAL 4.5 5.2 - - - +
201B ASP* 4.0 13.9 - - + +
232B CYS* 3.6 14.4 - - - +
234B GLN* 4.9 1.1 - - + +
277B PHE* 3.5 26.6 - - + -
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Residues in contact with THR 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 GLN 3.1 17.7 + - - -
108B GLU 4.2 0.4 - - - -
109B MSE 3.2 0.2 - - - -
110B ILE* 1.3 83.0 - - - +
112B HIS* 1.3 65.6 + - + +
114B PRO* 3.1 20.2 - - - +
115B LEU* 3.4 33.1 + - + +
134B VAL* 3.5 20.3 - - - +
137B GLU* 3.3 18.6 - - - +
138B VAL* 3.5 30.3 - - + +
199B ILE* 4.3 4.9 - - + -
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Residues in contact with HIS 112 (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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108B GLU* 2.9 27.4 + - + +
111B THR* 1.3 76.8 - - + +
113B LEU* 1.3 66.7 + - - +
114B PRO 3.3 0.7 - - - -
115B LEU 4.5 1.1 - - - +
116B CYS* 2.9 34.1 + - - +
137B GLU* 2.6 47.8 + - - +
140B ARG* 3.9 6.7 - - - -
141B HIS* 2.8 32.2 + + - -
296B ILE* 3.5 18.1 - - + +
307B LEU* 3.1 23.4 - - + +
310B TYR* 3.8 24.7 - + + -
315B HIS* 3.7 2.3 - - - -
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Residues in contact with LEU 113 (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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109B MSE 2.9 52.3 + - + +
112B HIS* 1.3 80.8 - - - +
114B PRO* 1.3 65.2 - - + +
117B SER* 2.9 23.4 + - - -
232B CYS* 4.1 3.4 - - - -
263B ALA* 3.8 12.6 - - + -
277B PHE* 3.6 32.3 - - + -
279B LEU* 3.4 37.0 - - + -
289B PHE* 4.1 1.8 - - - -
310B TYR* 4.9 0.7 - - + -
315B HIS* 3.5 23.0 - - + +
318B ALA* 4.8 3.4 - - + -
319B PHE* 4.5 6.7 - - + -
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Residues in contact with PRO 114 (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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110B ILE 3.0 23.8 - - - +
111B THR* 3.1 10.8 - - - +
113B LEU* 1.3 90.2 - - + +
115B LEU* 1.3 69.8 + - + +
116B CYS 2.8 5.2 + - - -
117B SER* 2.8 30.1 + - - -
118B ILE* 3.6 8.3 + - - +
197B ALA* 4.9 3.1 - - + -
198B VAL 5.5 0.4 - - - +
199B ILE* 5.0 6.7 - - + -
230B VAL* 3.9 24.7 - - + +
232B CYS* 3.9 23.6 - - + +
279B LEU* 4.0 7.2 - - + -
289B PHE* 4.3 2.2 - - + -
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Residues in contact with LEU 115 (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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111B THR* 3.4 38.9 + - + +
112B HIS* 4.6 0.2 - - - -
114B PRO* 1.3 84.6 - - + +
116B CYS* 1.3 58.8 + - - +
117B SER 3.5 0.2 - - - -
118B ILE* 3.8 12.1 - - + +
121B PRO* 4.1 14.7 - - + +
124B VAL* 4.0 15.3 - - + -
138B VAL* 3.8 21.8 - - + -
141B HIS* 3.5 32.4 - - + +
144B ILE* 5.0 0.7 - - + -
197B ALA* 3.6 30.7 - - + -
199B ILE* 4.8 4.0 - - + -
294B ASN* 3.2 21.1 + - - -
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Residues in contact with CYS 116 (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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112B HIS* 2.9 22.3 + - - +
114B PRO 2.8 1.4 + - - -
115B LEU* 1.3 76.1 - - - +
117B SER* 1.3 60.7 + - - +
118B ILE 3.5 1.6 - - - -
141B HIS* 4.0 10.1 - - - -
292B PRO* 3.0 18.8 - - + +
294B ASN 3.0 42.0 + - - +
295B PRO* 4.0 1.6 - - - -
296B ILE* 3.7 31.2 - - - -
310B TYR* 3.6 22.4 - - - +
315B HIS* 4.2 0.7 - - + -
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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