Contacts of the helix formed by residues 113 - 117 (chain D) in PDB entry 7C17
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 HIS 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1333C LEU* 2.4 50.7 + - + -
1334C GLY* 3.9 5.9 - - - -
111D THR 3.8 3.0 + - - -
112D ALA* 1.3 71.1 - - - +
114D ILE* 1.3 62.3 + - - +
115D TRP* 3.2 21.1 + - + +
116D PHE* 3.2 49.5 + + + +
117D LEU* 3.2 14.0 + - - +
237D MET 3.8 11.7 - - - +
238D ILE* 4.8 3.0 - - - +
239D LEU* 3.9 33.8 - - + +
307D LEU* 3.6 21.3 - - + +
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Residues in contact with ILE 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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112D ALA 3.4 4.9 + - - +
113D HIS* 1.3 69.4 - - - +
115D TRP* 1.3 64.7 + - - +
116D PHE 3.3 0.2 - - - -
117D LEU* 3.6 18.6 - - + -
118D LYS* 3.1 40.0 + - + +
300D GLN* 4.0 4.0 - - - +
304D ASP* 3.7 46.0 - - + +
307D LEU* 3.7 22.9 - - + +
308D ASP* 3.8 15.5 - - + +
311D ARG* 4.1 9.8 - - + -
312D ARG* 3.7 35.2 - - + -
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Residues in contact with TRP 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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1333C LEU* 3.6 34.7 - - + +
1335C ILE* 4.3 5.6 - - + -
113D HIS* 3.2 18.9 + + + +
114D ILE* 1.3 81.1 - - - +
116D PHE* 1.3 57.3 + - + +
117D LEU 3.3 0.4 - - - -
119D SER* 3.3 23.9 - - - -
122D SER 4.5 0.2 - - - +
307D LEU* 3.7 21.8 + - + +
308D ASP* 3.7 18.5 + - + +
311D ARG* 5.4 2.5 - - - +
328D ALA* 3.6 29.6 - - + +
331D ILE* 3.8 24.0 - - + -
1328D THR 4.4 0.4 - - - -
1329D THR* 3.6 33.7 - - + -
1332D LEU* 3.6 32.5 - - + -
1333D THR* 3.3 36.3 - - + +
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Residues in contact with PHE 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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1334C GLY 4.7 6.1 - - - -
1335C ILE* 4.3 11.4 - - + -
24D LEU* 3.8 21.8 - - + -
113D HIS* 3.2 45.4 + + + +
115D TRP* 1.3 74.6 - - + +
117D LEU* 1.3 56.8 + - - +
122D SER 2.9 21.9 - - - +
123D ARG* 5.3 3.1 - - + -
124D ILE* 3.3 21.0 - - + +
237D MET* 3.5 45.1 - - + -
1333D THR* 3.6 31.6 - - + -
1336D ALA* 4.2 7.6 - - + -
1337D VAL* 3.7 31.9 - - + -
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Residues in contact with LEU 117 (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 ALA* 3.8 12.8 - - + -
113D HIS 3.2 14.3 + - - +
114D ILE* 3.4 15.2 + - + -
115D TRP 3.3 1.0 + - - -
116D PHE* 1.3 79.2 - - - +
118D LYS* 1.3 62.6 + - + +
119D SER 3.5 2.0 - - - -
122D SER* 3.3 18.7 - - - -
124D ILE* 4.0 24.5 - - + +
132D LEU* 3.4 13.7 - - - +
135D ILE* 3.9 13.9 - - + -
139D LEU* 3.8 38.8 - - + -
300D GLN* 3.7 26.7 - - - +
312D ARG* 4.3 10.1 - - - +
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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