Contacts of the helix formed by residues 111 - 116 (chain D) 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 THR 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D GLN 3.0 20.7 + - - +
109D MSE 3.3 0.2 - - - -
110D ILE* 1.3 86.1 - - + +
112D HIS* 1.3 70.0 + - - +
114D PRO* 3.2 3.2 - - - +
115D LEU* 2.8 33.9 + - - +
134D VAL* 3.4 44.9 - - + +
137D GLU* 3.1 17.5 - - + +
138D VAL* 3.9 15.7 - - + -
199D ILE* 3.8 7.6 - - + +
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Residues in contact with HIS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D GLU* 3.5 36.2 + - - +
109D MSE 3.9 1.4 + - - -
111D THR* 1.3 82.4 + - - +
113D LEU* 1.3 68.3 + - - +
114D PRO 3.2 2.2 - - - -
115D LEU* 4.1 2.7 - - - -
116D CYS* 2.6 36.4 + - - +
137D GLU* 2.6 53.0 + - - +
140D ARG* 3.9 11.2 - - - -
141D HIS* 3.0 27.3 + + - -
296D ILE* 4.2 5.1 - - + +
307D LEU* 3.8 16.7 - - + +
310D TYR* 3.9 15.9 - + + -
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D MSE 3.1 51.9 + - + +
112D HIS* 1.3 79.3 - - - +
114D PRO* 1.4 63.8 - - + +
117D SER* 2.9 21.7 + - - -
232D CYS* 4.9 0.4 - - - -
263D ALA* 4.3 8.3 - - + -
277D PHE* 4.1 17.0 - - + -
279D LEU* 4.5 14.4 - - + -
289D PHE* 4.6 0.9 - - - -
310D TYR* 4.1 3.9 - - + -
315D HIS* 3.2 57.1 - - + +
318D ALA* 4.1 17.5 - - + -
319D PHE* 4.1 10.3 - - + -
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Residues in contact with PRO 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ILE 3.1 24.9 - - - +
111D THR* 3.2 10.1 - - - +
113D LEU* 1.4 93.0 - - + +
115D LEU* 1.3 68.0 + - + +
116D CYS 3.1 2.0 - - - -
117D SER* 2.9 27.6 + - - +
118D ILE* 3.6 9.0 + - - +
197D ALA* 5.6 1.6 - - + -
198D VAL 5.7 0.7 - - - +
199D ILE* 4.5 9.9 - - + -
230D VAL* 4.3 18.6 - - + +
232D CYS* 3.5 27.6 - - + -
279D LEU* 3.8 13.2 - - + -
289D PHE* 4.5 1.8 - - + -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D THR* 2.8 19.6 + - - +
114D PRO* 1.3 80.7 - - + +
116D CYS* 1.3 56.1 + - - +
117D SER 3.3 0.2 - - - -
118D ILE* 3.9 7.9 - - + +
121D PRO* 4.0 13.9 - - + +
124D VAL* 3.9 23.8 - - + -
138D VAL* 3.9 36.6 - - + +
141D HIS* 3.3 49.1 + - + +
144D ILE* 4.4 6.1 - - + -
197D ALA* 4.0 19.5 - - + -
199D ILE* 4.9 5.8 - - + -
294D ASN* 3.4 12.0 + - - -
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Residues in contact with CYS 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D HIS* 2.6 23.2 + - - +
113D LEU 4.3 1.8 - - - +
115D LEU* 1.3 72.7 - - - +
117D SER* 1.3 60.8 + - - +
141D HIS* 4.1 4.0 - - - -
292D PRO* 4.2 4.1 - - + +
293D LEU 3.6 3.6 + - - -
294D ASN* 2.9 48.7 + - - -
295D PRO* 4.1 5.4 - - - -
296D ILE* 3.7 28.9 - - - -
310D TYR* 3.3 35.9 - - - +
315D HIS* 4.5 2.0 - - + -
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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