Contacts of the helix formed by residues 129 - 141 (chain A) in PDB entry 2ZH7
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 ARG 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 3.2 34.9 - - + +
125A SER 5.4 0.4 - - - -
126A ALA* 2.8 33.7 + - - +
128A ASP* 1.3 75.5 - - - +
130A THR* 1.3 66.8 + - - +
131A PRO* 3.1 3.1 - - - -
132A PHE* 2.9 15.8 + - + +
133A HIS* 3.0 45.5 + - + +
218A ASP* 3.6 9.9 - - - -
220A VAL* 4.6 10.8 - - + -
221A ASP* 4.6 17.4 + - - +
224A ARG* 3.2 37.9 - - - +
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Residues in contact with THR 130 (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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45A VAL* 3.9 26.7 - - + -
46A GLY* 5.5 2.2 - - - +
50A ARG* 6.3 0.4 - - - +
63A PHE* 3.7 16.0 - - + -
126A ALA 3.7 6.6 + - - -
127A VAL* 3.2 18.6 + - - +
129A ARG* 1.3 78.8 - - - +
131A PRO* 1.3 63.7 - - - +
133A HIS* 3.3 14.9 + - + +
134A HIS* 3.0 21.1 + - - +
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Residues in contact with PRO 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 5.5 4.9 - - + -
45A VAL* 4.7 8.1 - - + -
63A PHE* 4.2 7.4 - - + -
65A LEU* 4.9 10.8 - - + -
114A CYS* 4.2 21.5 - - - -
115A TYR 5.3 3.8 - - - +
127A VAL 2.9 17.3 - - - +
128A ASP* 3.5 12.3 - - - +
129A ARG 3.1 5.2 - - - -
130A THR* 1.3 90.2 - - - +
132A PHE* 1.3 65.1 + - + +
134A HIS* 3.1 9.8 + - + +
135A LYS* 3.0 24.0 + - - +
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Residues in contact with PHE 132 (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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115A TYR 6.1 0.2 - - - -
117A LEU* 4.0 28.0 - - + -
118A LYS* 6.3 0.2 - - + -
119A GLU* 3.7 24.9 - - - -
120A PRO* 3.7 32.3 - - + -
123A ILE* 4.1 13.2 - - + -
128A ASP 3.3 26.2 - - - -
129A ARG* 2.9 11.4 + - - +
131A PRO* 1.3 75.7 - - + +
133A HIS* 1.3 56.6 + - - +
134A HIS 2.8 4.3 - - - -
135A LYS* 2.6 32.5 + - + +
136A TRP* 2.8 13.6 + - - +
220A VAL* 3.7 25.4 - - + -
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Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 5.8 0.9 - - - -
129A ARG* 3.0 44.2 + - + -
130A THR* 3.5 15.1 + - + +
132A PHE* 1.3 78.4 - - - +
134A HIS* 1.3 58.6 + - - +
136A TRP* 4.0 2.9 - - - +
137A LEU* 3.0 32.2 + - - +
173A TYR* 2.9 49.9 - + + -
218A ASP* 2.8 25.5 + - - -
220A VAL* 3.3 20.2 - - + +
224A ARG* 4.5 8.3 - - - -
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Residues in contact with HIS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 4.9 7.6 - - + -
44A PHE 3.6 15.5 + - - -
45A VAL* 3.9 21.0 - - + -
49A ALA* 3.4 25.2 - - + +
50A ARG* 2.9 49.0 + - + +
130A THR 3.0 12.1 + - - +
131A PRO 3.3 9.2 - - - +
132A PHE 2.7 2.4 + - - -
133A HIS* 1.3 75.7 - - - +
135A LYS* 1.3 61.1 + - + +
137A LEU* 2.9 3.6 + - - -
138A GLU* 2.7 62.2 + - + +
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Residues in contact with LYS 135 (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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131A PRO 3.0 14.1 + - - +
132A PHE* 2.6 17.6 + - + +
134A HIS* 1.3 77.7 - - + +
136A TRP* 1.3 60.9 + - - +
138A GLU* 3.0 45.9 - - - +
139A GLY* 4.2 2.1 + - - -
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Residues in contact with TRP 136 (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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132A PHE 2.8 16.5 + - - +
133A HIS* 4.1 3.6 - - - +
135A LYS* 1.3 74.9 - - - +
137A LEU* 1.3 88.8 + - + +
138A GLU 3.8 0.2 + - - -
139A GLY 4.2 0.9 + - - -
140A ARG* 3.2 71.4 + - - +
173A TYR* 5.4 1.6 - - - +
177A LEU* 4.0 4.9 - - + -
180A VAL* 3.9 12.1 - - + -
203A VAL* 3.9 20.2 - - + -
204A ALA* 5.2 8.4 - - - +
219A PRO* 3.3 45.9 - - + +
220A VAL* 4.4 15.5 - - + -
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Residues in contact with LEU 137 (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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50A ARG* 3.3 31.4 - - - +
133A HIS 3.0 16.2 + - - +
134A HIS 2.9 2.5 + - - +
136A TRP* 1.3 108.5 - - + +
138A GLU* 1.3 62.6 + - - +
139A GLY 3.3 0.9 - - - -
140A ARG* 4.1 0.9 - - - +
141A ILE* 3.0 34.2 + - + +
173A TYR* 3.5 31.2 - - + -
176A GLU* 3.4 24.2 - - + +
177A LEU* 3.8 13.9 - - + -
180A VAL* 4.4 12.6 - - + -
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Residues in contact with GLU 138 (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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50A ARG* 4.2 12.0 - - + +
134A HIS* 2.7 42.1 + - + +
135A LYS* 3.0 50.3 - - - +
137A LEU* 1.3 74.0 - - - +
139A GLY* 1.3 63.8 + - - +
141A ILE* 4.1 8.0 - - - +
142A LYS* 4.2 14.0 + - - +
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Residues in contact with GLY 139 (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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135A LYS 4.2 2.0 + - - -
136A TRP 4.2 3.8 + - - -
137A LEU 3.3 0.2 - - - -
138A GLU* 1.3 85.6 - - - +
140A ARG* 1.3 65.4 + - - +
141A ILE 3.5 0.4 + - - -
142A LYS* 3.9 13.6 - - - +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TRP* 3.2 78.4 + - + +
137A LEU 3.5 2.3 + - - +
139A GLY* 1.3 78.2 - - - +
141A ILE* 1.3 59.7 + - - +
142A LYS 3.4 2.0 + - - +
144A LYS* 3.3 24.6 + - - -
180A VAL* 4.3 21.9 - - + +
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Residues in contact with ILE 141 (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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50A ARG* 4.2 26.0 - - + +
52A THR* 4.3 8.5 - - + -
137A LEU* 3.0 27.0 + - + +
138A GLU 4.1 6.1 - - - +
140A ARG* 1.3 75.7 - - - +
142A LYS* 1.3 72.8 + - + +
143A GLY 3.1 0.2 + - - -
144A LYS* 3.0 31.1 + - + +
145A GLU* 3.9 7.0 + - - +
148A VAL* 3.4 31.6 - - + -
176A GLU* 3.9 20.0 - - + +
179A ILE* 4.3 6.3 - - + -
180A VAL* 4.2 19.7 - - + +
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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