Contacts of the helix formed by residues 115 - 120 (chain I) in PDB entry 2ZHX
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 LEU 115 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I LEU* 4.7 0.2 - - - -
80I SER 3.6 8.7 - - - +
81I PHE* 4.0 10.5 - - + +
82I SER* 2.5 44.5 + - - +
94I LEU* 4.2 5.4 - - + -
97I ILE* 6.3 0.2 - - + -
98I PHE* 3.7 36.6 - - + -
113I GLY 4.0 5.8 - - - +
114I ASP* 1.3 75.4 - - - +
116I THR* 1.3 66.2 + - - +
117I PRO* 3.2 3.4 - - - -
118I TRP* 2.9 51.1 + - + +
119I ALA 3.4 1.9 + - - -
125I LEU* 3.7 15.7 - - + +
226I LEU* 4.3 9.6 - - + -
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Residues in contact with THR 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLY 4.5 0.4 - - - +
204C SER* 4.1 10.1 - - - +
209C ARG* 3.3 38.0 - - - +
51I ARG* 3.1 35.0 + - - +
55I PHE* 4.7 5.4 - - + -
77I VAL* 5.7 0.3 - - - +
79I LEU* 4.1 11.0 - - - +
82I SER* 4.0 2.0 + - - -
114I ASP* 2.6 19.6 + - - -
115I LEU* 1.3 77.5 - - - +
117I PRO* 1.3 65.8 - - - +
119I ALA* 2.7 17.2 + - - +
120I GLN* 3.1 17.6 + - + +
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Residues in contact with PRO 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ARG* 3.9 12.1 - - - +
114I ASP* 3.6 13.5 - - - +
115I LEU 3.4 2.2 - - - +
116I THR* 1.3 91.8 - - - +
118I TRP* 1.3 64.9 + - + +
120I GLN* 2.8 33.2 + - + +
121I ARG* 3.2 39.0 + - - +
225I ARG 5.4 0.4 - - - +
226I LEU* 4.4 21.8 - - + +
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Residues in contact with TRP 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I ILE* 4.3 11.2 - - + -
97I ILE* 4.6 12.3 - - + -
98I PHE* 4.9 4.7 - + - -
101I TYR* 4.3 15.9 - + - -
115I LEU* 2.9 49.0 + - + +
117I PRO* 1.3 73.5 - - + +
119I ALA* 1.3 57.9 + - - +
121I ARG* 2.8 28.7 + - - +
123I VAL* 3.2 29.1 + - + +
125I LEU* 4.4 13.0 - - + -
168I TRP* 5.7 1.8 - + - -
207I PHE* 3.6 28.5 - + - -
222I ILE* 5.4 0.4 - - + -
224I TRP* 3.4 59.8 - + - +
225I ARG 4.1 0.2 - - - +
226I LEU* 3.4 34.7 - - + +
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Residues in contact with ALA 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I PHE* 3.7 42.7 - - + +
79I LEU* 4.0 25.1 - - + -
115I LEU 3.4 0.8 + - - -
116I THR 2.7 17.2 + - - +
118I TRP* 1.3 76.4 - - - +
120I GLN* 1.3 54.7 + - - +
121I ARG 3.0 4.2 + - - -
122I GLY* 3.6 7.6 + - - -
123I VAL 3.3 18.8 + - - +
125I LEU* 4.3 6.0 - - + +
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Residues in contact with GLN 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C GLU 3.0 17.8 - - - +
189C SER* 3.4 20.5 - - - +
190C PRO* 5.3 3.8 - - + +
199C ARG 5.1 6.2 - - - +
200C GLY* 3.1 27.9 + - - +
204C SER* 3.8 9.1 - - - -
209C ARG* 4.0 9.7 + - - -
55I PHE* 3.8 19.8 - - + -
59I ASN* 5.3 3.3 - - - +
116I THR* 3.1 11.1 + - - +
117I PRO* 2.8 43.0 + - + +
119I ALA* 1.3 71.1 - - - +
121I ARG* 1.3 63.1 + - + +
122I GLY 3.6 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
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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