Contacts of the helix formed by residues 119 - 127 (chain A) in PDB entry 1ZQ1
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 THR 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.4 26.1 + - + +
82A GLU 2.8 40.2 - - - +
83A ALA* 3.7 7.7 - - - +
118A PHE* 1.3 78.6 + - - +
120A ALA* 1.3 54.8 + - - +
121A GLU 3.5 3.8 - - - +
122A GLU* 2.7 45.2 + - - +
123A LEU* 2.8 13.5 + - - +
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Residues in contact with ALA 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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83A ALA 2.8 25.8 + - - +
84A LEU* 3.7 15.0 - - - -
85A ILE* 3.8 19.9 - - + +
118A PHE 3.7 3.0 + - - -
119A THR* 1.3 70.7 - - - +
121A GLU* 1.3 56.9 + - - +
123A LEU* 4.4 4.7 - - - +
124A ALA* 3.0 30.0 + - - +
131A PHE* 3.8 7.1 - - + -
136A VAL 4.7 2.5 - - - +
138A PRO* 3.8 21.6 - - + +
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Residues in contact with GLU 121 (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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80A HIS 4.0 2.3 - - - +
81A PHE* 3.1 42.2 - - + +
82A GLU* 3.1 51.8 + - + +
85A ILE* 5.0 8.3 - - + +
119A THR 3.2 0.4 - - - -
120A ALA* 1.3 76.7 - - - +
122A GLU* 1.3 59.4 + - - +
124A ALA* 3.6 7.3 - - + +
125A LYS* 3.5 19.2 + - - +
54C MET* 4.6 0.7 - - - +
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Residues in contact with GLU 122 (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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81A PHE* 3.4 36.2 - - + -
106A ARG* 3.0 42.3 + - - +
117A ALA* 3.6 26.3 - - + +
118A PHE 3.6 2.1 + - - -
119A THR* 2.7 37.6 + - - +
121A GLU* 1.3 76.8 - - - +
123A LEU* 1.3 57.3 + - - +
124A ALA 2.8 5.1 + - - -
125A LYS 3.2 1.0 + - - -
126A ALA* 2.8 35.3 + - - +
54C MET* 3.4 13.9 - - + +
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Residues in contact with LEU 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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96A ILE* 4.4 18.6 - - + -
103A ILE* 5.0 10.8 - - + +
104A ALA* 4.0 24.7 - - + -
117A ALA 4.0 12.6 - - - +
118A PHE* 4.0 19.7 - - + +
119A THR 2.8 19.7 + - - +
120A ALA* 4.0 4.5 - - - +
122A GLU* 1.3 70.9 - - - +
124A ALA* 1.3 57.2 + - - +
126A ALA* 4.4 1.3 - - - -
127A LEU* 2.8 38.3 + - + +
130A ILE* 4.3 8.1 - - + -
131A PHE* 3.3 13.8 - - + -
136A VAL* 5.2 1.3 - - + -
138A PRO* 3.7 28.5 - - + -
219A LEU* 5.0 7.9 - - + -
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Residues in contact with ALA 124 (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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85A ILE* 4.6 13.9 - - + -
120A ALA 3.0 18.0 + - - +
121A GLU* 3.6 10.8 - - - +
122A GLU 2.8 1.4 - - - -
123A LEU* 1.3 77.0 - - - +
125A LYS* 1.3 59.9 + - - +
128A PRO* 3.1 32.4 - - - +
131A PHE* 3.6 19.3 - - + -
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Residues in contact with LYS 125 (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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121A GLU 3.5 7.3 + - - +
122A GLU 3.2 1.2 + - - -
124A ALA* 1.3 80.0 - - - +
126A ALA* 1.3 63.4 + - - +
128A PRO* 4.0 8.8 - - - +
54C MET* 3.4 17.0 - - + -
58C GLY 3.2 28.9 - - - +
59C GLU* 4.5 1.5 - - - +
60C ILE* 3.3 41.4 - - + +
65C LEU* 5.4 6.3 - - - +
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Residues in contact with ALA 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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104A ALA* 4.3 20.4 - - + -
105A SER 5.6 0.9 - - - +
122A GLU 2.8 18.4 + - - +
123A LEU* 4.4 1.1 - - - -
125A LYS* 1.3 81.4 - - - +
127A LEU* 1.3 53.5 + - + +
128A PRO* 3.5 4.8 - - - +
51C ARG* 2.7 28.3 + - - +
54C MET* 3.7 24.6 - - + +
60C ILE* 5.5 1.6 - - - -
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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
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103A ILE* 5.0 4.9 - - + +
123A LEU* 2.8 27.2 + - + +
126A ALA* 1.3 81.9 - - + +
128A PRO* 1.3 60.5 - - - +
129A GLU* 3.4 31.0 - - + +
130A ILE* 3.0 20.9 - - + +
131A PHE* 3.8 0.2 - - - -
216A ALA* 3.9 18.4 - - + +
219A LEU* 3.1 48.5 - - + -
220A ILE* 3.8 9.4 - - + -
51C ARG* 3.9 10.8 - - - +
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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