Contacts of the helix formed by residues 115 - 120 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.8 1.8 - - - -
80A SER 3.7 8.1 - - - +
81A PHE* 4.0 8.1 - - + -
82A SER* 2.8 43.3 + - - +
94A LEU* 4.1 9.6 - - + -
97A ILE* 6.2 0.2 - - + -
98A PHE* 3.6 34.8 - - + -
113A GLY 4.0 6.5 - - - +
114A ASP* 1.3 74.1 - - - +
116A THR* 1.3 67.9 + - - +
117A PRO* 3.1 5.2 - - - -
118A TRP* 2.8 50.5 + - + +
119A ALA* 3.4 2.1 + - - +
125A LEU* 3.8 13.6 - - + +
226A LEU* 3.9 12.1 - - + -
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Residues in contact with THR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ARG* 2.9 32.2 + - - +
55A PHE* 4.9 4.0 - - + -
77A VAL* 5.9 0.5 - - - +
79A LEU* 4.2 11.9 - - - +
82A SER* 4.2 2.1 + - - -
114A ASP* 2.6 23.3 + - - -
115A LEU* 1.3 74.7 - - - +
117A PRO* 1.4 61.6 - - - +
119A ALA* 2.7 27.4 + - - +
120A GLN* 3.1 20.8 + - + +
203K GLY 4.2 1.8 - - - +
204K SER* 4.0 10.8 - - - +
209K ARG* 3.5 31.4 + - - +
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Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ASP* 3.8 11.0 - - - +
115A LEU* 3.2 4.3 - - - +
116A THR* 1.4 93.9 - - - +
118A TRP* 1.3 64.8 + - + +
120A GLN* 3.0 32.7 + - + +
121A ARG* 3.2 39.7 - - - +
225A ARG 5.3 0.4 - - - +
226A LEU* 4.1 27.1 - - + +
209K ARG* 4.6 4.9 - - - +
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Residues in contact with TRP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.5 9.0 - - + -
94A LEU* 6.2 0.2 - - + -
97A ILE* 4.8 8.1 - - + -
98A PHE* 4.6 13.9 - + - -
101A TYR* 4.0 21.1 - + - -
115A LEU* 2.8 49.5 + - + +
117A PRO* 1.3 73.5 - - + +
119A ALA* 1.3 58.3 + - - +
121A ARG* 2.9 27.4 + - - +
123A VAL* 3.3 29.0 + - + +
125A LEU* 4.4 11.7 - - + -
168A TRP* 5.8 0.9 - + - -
207A PHE* 3.7 25.1 - + - -
222A ILE* 5.1 1.3 - - + -
224A TRP* 3.0 68.6 - + - +
225A ARG 3.7 1.8 - - - +
226A LEU* 3.9 22.2 - - + +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.7 41.7 - - + +
79A LEU* 3.9 26.9 - - + -
115A LEU 3.4 2.1 + - - +
116A THR 2.7 19.1 + - - +
118A TRP* 1.3 74.5 - - - +
120A GLN* 1.3 53.4 + - - +
121A ARG 3.1 3.5 + - - -
122A GLY* 3.5 9.9 + - - -
123A VAL 3.4 19.3 + - - +
125A LEU* 4.8 4.0 - - + +
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.7 20.8 - - + -
59A ASN* 5.2 3.8 - - - +
116A THR* 3.1 18.9 + - + +
117A PRO* 3.2 30.4 - - + +
119A ALA* 1.3 75.1 - - - +
121A ARG* 1.3 64.0 + - + +
122A GLY 3.6 0.7 - - - -
188K GLU 3.3 20.4 - - - +
189K SER* 3.9 7.8 - - - -
190K PRO* 4.5 5.3 - - + +
199K ARG 3.7 16.5 - - - +
200K GLY* 2.5 39.0 + - - +
204K SER* 3.9 19.0 - - - +
209K ARG* 4.4 3.3 + - - -
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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