Contacts of the helix formed by residues 102 - 116 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B TRP* 3.5 28.3 - - + -
86C TYR* 5.0 2.5 - - + -
99C THR* 2.9 19.3 + - - +
101C ARG* 1.3 76.2 - - + +
103C GLU* 1.3 61.6 + - - +
104C CYS* 3.1 8.1 + - - +
105C ALA* 3.4 17.1 + - - +
106C TYR* 4.2 1.7 + - - +
267C VAL* 4.0 7.3 - - - +
268C PRO* 3.1 19.1 - - + +
269C THR* 2.6 49.3 + - - -
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.0 12.4 - - + +
99C THR 2.7 29.0 + - - +
100C GLU* 3.1 34.7 + - - +
101C ARG 3.8 0.6 - - - -
102C ASP* 1.3 71.3 - - - +
104C CYS* 1.3 68.3 + - + +
105C ALA 3.3 0.4 + - - -
106C TYR* 3.6 5.9 + - - +
107C GLN* 2.9 53.5 + - + +
131C ASP* 3.0 20.3 - - - +
136C ARG* 4.5 9.4 + - - +
166C ASP* 6.2 0.2 - - - +
167C VAL* 3.8 18.9 - - - +
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Residues in contact with CYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.8 27.4 - - - -
324B PHE* 5.3 2.9 - - - -
100C GLU 5.3 1.0 + - - +
101C ARG 4.4 4.5 - - - -
102C ASP* 4.1 4.9 - - - -
103C GLU* 1.3 82.9 - - + +
105C ALA* 1.3 67.1 + - - +
107C GLN* 5.0 2.0 - - - -
108C GLU* 2.7 61.2 + - - +
136C ARG* 5.2 4.9 - - - +
308C LYS* 4.0 26.7 - - + +
309C PHE* 4.2 9.0 - - - -
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.9 7.2 - - + -
102C ASP 3.4 11.4 + - - +
103C GLU 3.3 0.2 - - - -
104C CYS* 1.3 81.5 - - - +
106C TYR* 1.3 58.2 + - - +
108C GLU* 4.2 0.2 - - - +
109C MSE 2.9 37.1 + - - +
265C THR* 5.0 0.2 - - - +
266C SER 3.4 25.6 - - - +
267C VAL* 4.2 6.3 - - + -
309C PHE* 3.5 31.2 - - + -
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Residues in contact with TYR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASP 4.2 1.5 + - - +
103C GLU* 3.6 8.3 + - - +
104C CYS 3.4 0.2 - - - -
105C ALA* 1.3 76.5 - - - +
107C GLN* 1.3 73.6 + - + +
109C MSE 3.2 3.1 + - - -
110C ILE* 2.8 57.2 + - + +
134C VAL* 4.7 2.0 - - + -
201C ASP* 2.8 32.9 + - - -
202C SER 4.3 3.3 + - - -
234C GLN* 3.5 27.0 - - + +
267C VAL* 4.1 15.9 - - + +
270C TYR* 3.5 42.0 - + + +
275C ILE* 4.0 9.2 - - + -
277C PHE* 3.5 30.5 - + - -
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Residues in contact with GLN 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.9 2.7 - - + +
103C GLU* 2.9 36.9 + - + +
104C CYS 4.4 0.4 - - - +
106C TYR* 1.3 81.8 - - + +
108C GLU* 1.3 61.9 + - - +
110C ILE* 3.4 9.0 - - - +
111C THR* 3.0 30.5 + - - -
131C ASP* 2.6 40.6 + - - -
133C GLY* 3.1 14.2 - - - -
134C VAL* 3.2 24.3 - - + +
136C ARG* 2.8 26.3 + - - +
137C GLU* 3.6 9.6 - - + +
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Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C CYS* 2.7 34.1 + - - +
105C ALA 4.2 0.9 - - - +
107C GLN* 1.3 74.1 - - + +
109C MSE 1.3 58.5 + - + +
112C HIS* 2.9 43.3 + - + +
137C GLU* 3.5 30.1 - - - +
140C ARG* 4.7 4.2 + - - -
307C LEU* 4.1 8.1 - - + +
308C LYS* 3.2 31.4 + - - +
309C PHE* 2.8 26.9 + - + -
310C TYR* 2.8 27.4 + - + +
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Residues in contact with MSE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA 2.9 27.4 + - - +
106C TYR 3.9 0.9 - - - +
108C GLU* 1.3 71.3 - - - +
110C ILE* 1.3 66.3 + - - +
111C THR 3.2 1.6 - - - -
113C LEU* 3.1 41.9 + - + +
264C TRP 5.2 0.2 - - - +
265C THR* 3.6 25.8 - - + +
277C PHE* 3.9 17.3 - - + -
309C PHE* 3.9 15.9 - - + -
310C TYR* 3.6 28.5 - - - -
314C ILE* 3.4 44.6 - - + +
315C HIS* 4.6 2.7 - - - +
318C ALA* 4.1 15.7 - - + -
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Residues in contact with ILE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C TYR* 2.8 55.3 + - + +
107C GLN* 3.4 12.8 - - - +
109C MSE 1.3 72.2 - - - +
111C THR* 1.3 68.2 + - - +
114C PRO* 3.3 19.1 - - - +
134C VAL* 3.8 16.6 - - + -
199C ILE* 3.9 23.5 - - + +
200C VAL 4.2 12.1 - - - +
201C ASP* 4.0 6.3 - - + +
232C CYS* 3.5 15.4 - - - +
234C GLN 4.6 2.9 - - - +
277C PHE* 3.4 29.1 - - + -
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Residues in contact with THR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLN 3.0 18.4 + - - -
108C GLU 4.1 1.3 - - - -
109C MSE 3.2 0.2 - - - -
110C ILE* 1.3 81.2 - - - +
112C HIS* 1.3 70.2 + - + +
114C PRO* 3.1 18.9 - - - +
115C LEU* 3.1 31.9 - - + +
134C VAL* 3.1 25.3 + - - +
137C GLU* 3.4 15.8 - - + +
138C VAL* 3.6 30.3 - - + +
199C ILE* 4.0 5.4 - - - -
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Residues in contact with HIS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLU* 2.9 34.0 + - + +
111C THR* 1.3 79.0 - - + +
113C LEU* 1.3 66.3 + - - +
114C PRO 3.1 1.8 - - - -
115C LEU 4.1 0.4 - - - -
116C CYS* 3.1 43.0 + - - +
137C GLU* 2.6 45.7 + - - +
140C ARG* 3.6 10.9 - - - -
141C HIS* 2.8 35.4 + + - -
296C ILE* 3.7 16.3 - - + +
307C LEU* 5.0 2.2 - - + +
310C TYR* 3.6 22.9 - + + -
315C HIS* 3.9 1.9 - - - -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C MSE 3.1 43.2 + - + +
112C HIS* 1.3 75.7 - - - +
114C PRO* 1.3 61.3 - - + +
117C SER* 2.5 30.0 + - - -
232C CYS* 5.0 0.9 - - - -
263C ALA* 4.2 15.5 - - + -
264C TRP 6.1 0.2 - - - -
265C THR* 5.9 0.4 - - - -
277C PHE* 4.0 22.9 - - + -
279C LEU* 4.3 13.9 - - + +
289C PHE* 4.2 4.3 - - - -
310C TYR* 4.2 2.4 - - + -
315C HIS* 3.5 48.4 + - + +
318C ALA* 4.4 8.5 - - + -
319C PHE* 3.8 14.3 - - + -
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Residues in contact with PRO 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ILE 3.3 21.1 - - - +
111C THR* 3.1 14.8 - - - +
113C LEU* 1.3 95.6 - - + +
115C LEU* 1.3 77.9 + - + +
117C SER* 2.9 20.2 + - - -
118C ILE* 3.4 6.8 + - - +
197C ALA* 5.3 1.1 - - + -
198C VAL 5.8 0.7 - - - +
199C ILE* 4.5 9.0 - - + -
230C VAL* 3.9 25.7 - - + +
232C CYS* 3.8 23.6 - - + +
279C LEU* 3.9 9.4 - - + -
289C PHE* 4.5 1.3 - - + -
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C THR* 3.1 29.7 + - + +
112C HIS* 4.6 0.2 - - - -
114C PRO* 1.3 73.9 - - + +
116C CYS* 1.3 52.2 + - - +
117C SER 2.8 4.7 - - - -
118C ILE* 2.6 46.0 + - + +
121C PRO* 4.3 21.0 - - + +
124C VAL* 4.1 13.0 - - + -
138C VAL* 4.2 19.3 - - + -
141C HIS* 3.5 42.8 - - + +
144C ILE* 4.9 2.2 - - + -
197C ALA* 3.9 26.5 - - + -
199C ILE* 4.8 4.0 - - + -
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Residues in contact with CYS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C HIS* 3.1 40.2 + - - +
115C LEU* 1.3 78.5 - - - +
117C SER* 1.3 58.8 + - - +
118C ILE 3.3 4.4 + - - +
141C HIS* 3.9 9.4 - - - -
292C PRO* 4.5 4.3 - - + -
293C LEU* 3.4 4.7 + - - +
294C ASN* 3.2 47.2 + - - +
295C PRO* 3.7 1.8 - - + -
296C ILE* 3.6 30.1 - - - -
310C TYR* 3.6 12.8 - - - +
315C HIS* 4.6 0.4 - - + -
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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