Contacts of the helix formed by residues 118 - 130 (chain A) in PDB entry 5ZCJ
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA* 3.7 1.1 - - - -
35A ALA 5.9 0.2 - - - +
117A LEU* 1.3 76.9 - - - +
119A LEU* 1.3 60.4 + - - +
120A GLU* 3.6 10.0 + - - +
121A GLN* 2.9 42.8 + - - +
122A LEU* 2.8 26.7 + - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA* 3.7 19.3 - - + +
35A ALA 4.0 11.2 + - - +
36A ASN* 3.4 40.8 - - - +
37A PRO* 4.2 12.6 - - + -
38A GLY 5.5 0.2 - - - +
49A SER* 4.4 3.4 - - - -
118A THR* 1.3 72.9 - - - +
120A GLU* 1.3 57.2 + - - +
122A LEU* 3.3 12.3 + - + +
123A HIS* 2.9 29.0 + - + +
144A ARG* 4.1 18.2 - - - +
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Residues in contact with GLU 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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118A THR* 3.1 8.8 + - - +
119A LEU* 1.3 79.4 - - - +
121A GLN* 1.3 61.2 + - - +
123A HIS* 3.4 6.5 + - - +
124A ALA* 3.0 26.9 + - + +
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Residues in contact with GLN 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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117A LEU* 3.4 28.3 - - + +
118A THR* 2.9 47.5 + - - +
120A GLU* 1.3 80.0 - - - +
122A LEU* 1.3 65.8 + - - +
124A ALA* 3.1 9.5 + - - +
125A VAL* 3.0 25.5 + - - +
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Residues in contact with LEU 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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32A LEU* 3.7 28.0 - - + +
33A TYR* 3.8 22.7 - - - +
34A ALA* 4.2 4.0 - - + -
49A SER* 3.9 29.4 - - - +
51A LEU* 3.8 25.7 - - + +
117A LEU* 4.1 10.2 - - + +
118A THR 2.8 12.7 + - - +
119A LEU* 3.6 13.7 - - + +
121A GLN* 1.3 76.7 - - - +
123A HIS* 1.3 61.8 + - - +
125A VAL* 3.1 6.9 + - - +
126A GLU* 3.1 22.1 + - - +
144A ARG* 4.0 22.2 - - - +
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Residues in contact with HIS 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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119A LEU* 2.9 17.8 + - + +
120A GLU* 3.7 7.4 - - + +
121A GLN 3.3 0.2 - - - -
122A LEU* 1.3 76.5 - - - +
124A ALA* 1.3 57.1 + - - +
126A GLU* 3.1 24.3 + - + +
127A ILE* 2.9 45.7 + - + +
144A ARG* 4.1 6.9 - - - +
130B VAL 2.7 28.6 + - - -
131B HIS* 4.9 8.1 - - - -
132B SER 6.1 0.4 - - - -
135B HIS* 3.8 11.8 - + - -
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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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88A CYS* 4.7 1.1 - - - -
120A GLU* 3.0 14.9 + - + +
121A GLN* 3.1 12.3 + - - +
123A HIS* 1.3 75.7 - - - +
125A VAL* 1.3 58.9 + - + +
127A ILE* 3.4 12.2 + - + +
128A SER* 3.0 28.9 + - - -
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Residues in contact with VAL 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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32A LEU* 4.2 2.7 - - + -
51A LEU* 3.8 20.6 - - + -
86A LEU* 3.9 32.3 - - + +
88A CYS* 4.0 16.6 - - - -
89A LEU* 3.8 25.6 - - + -
117A LEU* 4.0 12.8 - - + -
121A GLN 3.0 18.1 + - - +
122A LEU 3.1 8.9 + - - +
124A ALA* 1.3 75.9 - - - +
126A GLU* 1.3 59.7 + - - +
128A SER* 3.2 2.4 + - - -
129A ALA* 2.8 28.1 + - - +
142A LEU* 4.6 0.2 - - + -
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Residues in contact with GLU 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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51A LEU* 3.5 20.0 - - + +
122A LEU 3.1 11.8 + - - +
123A HIS* 3.1 13.6 + - - +
125A VAL* 1.3 76.6 - - - +
127A ILE* 1.3 61.5 + - - +
129A ALA* 3.2 10.7 + - - +
130A VAL* 3.4 19.8 + - - +
142A LEU* 4.2 18.0 - - + +
143A VAL 5.6 0.2 - - - -
144A ARG* 2.7 57.8 + - - +
130B VAL* 3.7 14.8 - - + -
135B HIS* 2.8 24.3 + - + -
140B LEU 5.0 0.9 - - - +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A HIS* 2.9 49.5 + - + +
124A ALA* 3.8 8.7 - - - +
126A GLU* 1.3 74.4 - - - +
128A SER* 1.3 63.4 + - - +
130A VAL* 3.2 8.3 - - - +
131A HIS* 3.1 34.0 - - + +
130B VAL* 4.1 13.7 - - + -
131B HIS* 3.5 41.1 - - + +
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Residues in contact with SER 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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86A LEU 2.6 24.8 + - - +
87A GLY* 3.2 21.1 + - - -
88A CYS* 3.7 15.7 - - - -
124A ALA 3.0 17.5 + - - -
125A VAL 3.2 0.9 + - - -
127A ILE* 1.3 78.0 - - - +
129A ALA* 1.3 62.8 + - - +
131A HIS* 3.2 16.9 + - - +
132A SER* 3.4 8.1 + - - -
133A ARG* 5.4 0.2 + - - -
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Residues in contact with ALA 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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85A GLY 4.2 2.6 - - - +
86A LEU* 3.3 20.2 + - + -
125A VAL 2.8 16.2 + - - +
126A GLU 3.2 6.9 + - - +
128A SER* 1.3 78.5 - - - +
130A VAL* 1.3 57.9 + - + +
132A SER* 2.9 29.4 + - - -
135A HIS* 3.6 8.1 + - - +
139A VAL* 6.3 0.2 - - + -
142A LEU* 3.7 32.3 - - + -
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Residues in contact with VAL 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 GLU 3.4 13.2 - - - +
127A ILE 3.2 17.7 - - - +
129A ALA* 1.3 77.5 - - + +
131A HIS* 1.3 68.7 + - + +
132A SER 3.4 0.4 - - - -
135A HIS* 3.7 24.6 - - + +
123B HIS* 2.7 32.8 + - - +
126B GLU* 4.5 11.2 - - + +
127B ILE* 4.1 22.0 - - + -
130B VAL* 4.4 22.0 - - + -
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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