Contacts of the helix formed by residues 119 - 135 (chain A) in PDB entry 3ZG2
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 PRO 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 2.9 17.3 - - - +
113A GLY* 5.1 1.6 - - - -
117A ALA 3.5 4.2 - - - +
118A ALA* 1.3 80.4 - - - +
120A TYR* 1.3 57.0 + - - +
121A PRO* 3.3 9.4 - - + -
122A ARG* 2.9 34.6 + - + +
123A MET 2.7 30.7 + - - -
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Residues in contact with TYR 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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94A ASN* 3.5 46.6 + - + +
95A GLU* 5.0 15.5 - - + +
98A SER* 2.3 35.5 + - - -
99A PRO* 3.3 12.1 - - + +
100A ARG* 2.9 29.6 - - + +
119A PRO* 1.3 69.6 - - - +
121A PRO* 1.3 73.1 - - + +
123A MET* 3.3 34.5 - - + +
124A ARG* 2.9 26.7 + - - +
364A LYS* 3.8 18.7 + - - -
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Residues in contact with PRO 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PRO* 3.4 11.4 - - + -
120A TYR* 1.3 94.6 - - + +
122A ARG* 1.3 56.3 + - - +
124A ARG* 3.5 5.3 - - + +
125A GLU* 2.9 37.5 + - - +
271A ARG* 6.3 1.3 - - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLY* 3.4 13.3 + - - -
118A ALA* 3.1 17.5 - - + -
119A PRO* 2.9 34.2 + - + +
121A PRO* 1.3 73.9 - - - +
123A MET* 1.3 63.6 + - - +
125A GLU* 3.1 16.6 + - - +
126A GLN* 2.8 64.0 + - - +
270A TYR* 3.8 21.9 + - + -
280A GLU* 3.5 26.9 + - - -
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Residues in contact with MET 123 (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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94A ASN* 5.1 4.5 - - - +
99A PRO* 4.8 2.2 - - + -
100A ARG* 4.0 4.7 - - - +
115A ALA* 3.2 27.7 - - - +
116A TYR* 3.1 53.4 - - + -
118A ALA* 3.9 3.6 - - - +
119A PRO 2.7 19.3 + - - +
120A TYR* 3.3 40.6 - - + +
122A ARG* 1.3 72.9 - - - +
124A ARG* 1.3 66.1 + - + +
126A GLN* 3.0 9.6 + - - +
127A LEU* 3.0 45.1 + - + +
420A HIS* 6.0 2.5 - - - -
1480A HEM 5.1 0.9 - - - +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN* 5.4 6.5 - - - +
120A TYR 2.9 21.1 + - - +
121A PRO* 3.5 5.4 - - + +
123A MET* 1.3 82.3 - - + +
125A GLU* 1.3 65.1 + - + +
126A GLN 3.2 0.2 + - - -
127A LEU* 3.2 20.7 + - - +
128A ASN* 2.9 57.1 + - - +
419A VAL* 3.9 22.2 + - - +
420A HIS* 4.5 8.9 + - - -
423A ILE* 6.0 3.6 - - - +
1480A HEM 4.1 15.0 + - - -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 2.9 32.5 + - - +
122A ARG* 3.3 18.2 + - - +
124A ARG* 1.3 78.7 - - + +
126A GLN* 1.3 63.2 + - - +
128A ASN* 3.3 11.4 + - - +
129A PHE* 3.2 29.8 + - + -
270A TYR* 3.4 26.3 - - + +
271A ARG* 2.9 54.8 + - + +
272A ASP* 5.4 3.1 - - - +
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Residues in contact with GLN 126 (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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113A GLY 3.2 13.7 + - - -
114A VAL* 3.6 10.4 - - - +
115A ALA* 2.8 29.9 + - - -
118A ALA* 3.7 1.5 - - - +
122A ARG* 2.8 48.1 + - - +
123A MET* 3.0 7.2 + - - +
125A GLU* 1.3 70.4 - - - +
127A LEU* 1.3 65.9 + - + +
129A PHE* 2.9 29.9 + - + +
130A LEU 3.2 4.3 + - - -
270A TYR* 3.7 13.7 - - - +
276A MET* 4.1 12.3 - - + -
280A GLU* 3.5 12.4 + - - -
284A MET* 3.7 22.5 - - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 6.0 2.9 - - - -
116A TYR* 5.8 0.2 - - + -
123A MET* 3.0 47.7 + - + +
124A ARG* 3.7 31.2 - - - +
126A GLN* 1.3 76.2 - - + +
128A ASN* 1.3 51.2 + - - +
130A LEU* 3.4 8.2 + - + +
131A ALA* 2.7 36.8 + - - +
284A MET* 4.7 2.7 - - + +
420A HIS* 6.3 0.4 - - + -
423A ILE* 3.9 9.1 - - + +
1480A HEM 3.5 53.2 - - + +
1490A UDO 3.7 18.6 - - + -
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Residues in contact with ASN 128 (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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124A ARG* 2.9 46.6 + - - +
125A GLU* 3.3 11.3 - - - +
126A GLN 3.1 0.2 - - - -
127A LEU* 1.3 72.3 - - - +
129A PHE* 1.3 62.6 + - + +
131A ALA* 3.3 7.6 - - - +
132A GLU* 2.8 50.0 + - - +
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Residues in contact with PHE 129 (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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125A GLU* 3.4 16.2 - - + -
126A GLN* 2.9 24.3 + - - +
128A ASN* 1.3 81.6 - - + +
130A LEU* 1.3 65.2 + - - +
132A GLU* 3.0 16.9 + - - +
133A GLU* 3.2 14.7 + - - +
265A LEU* 3.7 20.2 - - + -
268A ALA* 3.7 23.8 - - + -
269A VAL 3.8 23.6 - - - -
270A TYR* 3.5 46.9 - + - -
276A MET* 4.0 17.9 - - + -
284A MET* 6.0 0.2 - - + -
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Residues in contact with LEU 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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126A GLN 3.2 1.2 + - - -
127A LEU* 3.6 7.2 - - + +
129A PHE* 1.3 79.0 - - - +
131A ALA* 1.3 63.7 + - - +
133A GLU* 2.9 19.5 + - - +
134A LEU* 3.1 42.8 + - + +
183A LEU* 6.5 0.2 - - + -
261A LEU* 3.7 19.1 - - + -
265A LEU* 4.1 4.6 - - + +
284A MET* 3.6 32.3 - - + +
288A ALA* 3.5 37.2 - - + +
423A ILE* 3.8 17.7 - - + -
1480A HEM 4.3 12.3 - - + -
1490A UDO 4.7 5.2 - - + -
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Residues in contact with ALA 131 (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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127A LEU 2.7 23.0 + - - +
128A ASN* 3.3 11.0 - - - +
130A LEU* 1.3 72.8 - - - +
132A GLU* 1.3 59.7 + - + +
134A LEU* 3.0 21.4 + - - +
135A THR* 3.0 17.5 + - + +
423A ILE* 4.1 25.1 - - + +
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Residues in contact with GLU 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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128A ASN* 2.8 39.5 + - - +
129A PHE* 3.0 9.6 + - - +
131A ALA* 1.3 73.8 - - + +
133A GLU* 1.3 62.7 + - - +
134A LEU 3.4 0.2 - - - -
135A THR* 3.2 27.6 + - + -
138A LYS* 3.3 17.7 + - - +
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Residues in contact with GLU 133 (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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129A PHE 3.5 15.8 - - - +
130A LEU* 2.9 10.9 + - - +
132A GLU* 1.3 84.0 - - - +
134A LEU* 1.3 57.6 + - + +
135A THR 3.3 1.6 - - - -
138A LYS* 3.2 34.6 + - - +
139A PHE* 5.1 1.0 - - - -
142A PHE* 5.1 0.9 - - - -
183A LEU* 5.0 8.7 - - + +
259A SER* 4.4 6.9 + - - +
260A ASP 3.7 15.9 - - - +
261A LEU* 3.8 36.7 - - + +
264A GLY* 3.1 31.7 - - - +
265A LEU* 4.4 4.4 - - + +
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Residues in contact with LEU 134 (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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130A LEU* 3.1 40.8 + - + +
131A ALA 3.0 7.1 + - - +
133A GLU* 1.3 77.6 - - + +
135A THR* 1.3 61.0 + - - +
139A PHE* 2.8 31.3 - - + -
183A LEU* 4.4 23.8 - - + -
261A LEU* 5.8 0.7 - - + -
288A ALA* 6.2 0.2 - - + -
423A ILE* 4.4 24.0 - - + +
426A LYS* 4.5 5.9 - - - +
427A PHE* 4.0 27.5 - - + +
1480A HEM 3.4 35.9 - - + -
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Residues in contact with THR 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 ALA 3.0 18.8 - - - +
132A GLU* 3.2 27.2 + - + +
133A GLU 3.3 0.8 - - - -
134A LEU* 1.3 82.8 - - - +
136A ILE* 1.3 58.6 + - - +
137A ALA* 2.9 26.3 + - - +
138A LYS* 3.0 17.8 + - - +
139A PHE* 3.5 7.3 - - - -
426A LYS* 4.3 13.2 - - - +
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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
------------------------------------------------------------
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