Contacts of the helix formed by residues 129 - 140 (chain A) in PDB entry 4KN1
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 CYS 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A PRO 3.6 0.6 + - - -
128A LEU* 1.3 74.5 - - - +
130A LYS* 1.3 65.4 + - - +
132A ASP* 3.1 17.8 + - + +
133A CYS* 3.3 8.8 + - - +
196A TYR 3.8 1.1 - - - -
198A ARG* 4.0 28.5 - - + +
199A GLY 5.0 0.2 - - - -
203A CYS* 2.0 62.1 - - - -
204A ILE 3.0 16.0 + - - +
205A GLN* 3.5 19.7 - - + -
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Residues in contact with LYS 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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128A LEU 3.3 2.2 + - - -
129A CYS* 1.3 72.7 - - - +
131A GLU* 1.3 77.8 + - + +
133A CYS* 3.3 4.1 + - - +
134A GLN* 2.8 29.0 + - - +
179A PRO* 5.8 0.2 - - - +
193A VAL* 4.1 17.4 - - + +
194A SER 3.2 13.2 + - - +
195A ASN* 2.9 47.1 + - - +
196A TYR 3.4 14.9 + - - +
197A SER* 4.4 4.3 - - - -
1B NAG 3.8 23.2 + - - -
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Residues in contact with GLU 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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129A CYS 3.2 0.2 + - - -
130A LYS* 1.3 86.8 + - + +
132A ASP* 1.3 61.5 + - - +
134A GLN* 3.6 7.2 - - - +
135A ARG* 2.8 34.0 + - - +
197A SER* 2.9 30.7 - - - -
198A ARG* 2.8 45.4 + - + +
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Residues in contact with ASP 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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93A HIS* 5.3 1.2 + - - -
128A LEU* 4.1 15.3 - - + -
129A CYS* 3.1 12.3 + - - +
131A GLU* 1.3 77.5 - - - +
133A CYS* 1.3 57.7 + - - +
135A ARG* 3.6 4.3 + - - +
136A TRP* 3.1 30.2 + - - +
198A ARG* 2.6 34.5 + - - +
205A GLN* 3.4 6.9 - - - -
206A MET* 2.5 41.5 + - + +
207A TRP* 3.1 20.0 + - + +
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Residues in contact with CYS 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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128A LEU* 4.2 7.1 - - + +
129A CYS 3.3 8.0 + - - +
130A LYS* 3.3 11.6 + - - +
131A GLU 3.2 0.2 - - - -
132A ASP* 1.3 77.1 - - - +
134A GLN* 1.3 65.7 + - - +
136A TRP* 3.4 3.0 + - - +
137A TRP* 3.0 26.0 + - - +
179A PRO* 3.2 30.7 - - + -
183A CYS* 2.0 48.6 - - + -
193A VAL* 4.0 15.9 - - + -
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Residues in contact with GLN 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 LYS 2.8 21.2 + - - +
131A GLU* 3.6 8.3 - - - +
133A CYS* 1.3 74.6 - - - +
135A ARG* 1.3 57.2 + - - +
137A TRP* 3.5 16.2 + - - +
138A GLU* 2.9 69.7 + - - +
179A PRO* 3.6 22.0 - - + +
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Residues in contact with ARG 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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92A ARG* 3.5 21.8 - - - +
93A HIS* 3.7 17.0 + - + -
131A GLU 2.8 20.2 + - - +
132A ASP* 4.0 4.7 - - - +
134A GLN* 1.3 71.4 - - - +
136A TRP* 1.3 60.4 + - - +
138A GLU* 3.4 12.7 + - - -
139A ASP* 2.9 54.5 + - - +
207A TRP* 6.3 0.9 - - + -
304A CL 3.5 17.8 - - - +
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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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93A HIS* 3.3 40.6 - - + +
94A PHE* 3.6 34.5 - + - -
97A ASP* 3.7 24.7 - - + -
128A LEU* 4.7 3.6 - - + -
132A ASP 3.1 20.6 + - - +
133A CYS 3.5 4.7 - - - +
135A ARG* 1.3 78.7 - - - +
137A TRP* 1.3 63.4 + - - +
139A ASP* 3.2 7.6 + - - +
140A CYS* 3.3 20.3 + - - -
182A LEU* 3.7 15.3 - - + +
183A CYS* 4.2 20.6 - - - -
186A LEU* 3.6 33.0 - - + -
191A TYR* 4.1 19.3 - + - -
206A MET* 3.7 26.7 - - + -
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Residues in contact with TRP 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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133A CYS 3.0 14.3 + - - +
134A GLN* 3.7 14.6 - - - +
136A TRP* 1.3 78.6 - - - +
138A GLU* 1.3 79.9 + - + +
140A CYS* 3.3 12.9 + - - +
141A HIS* 3.2 56.2 + + - -
172A PHE* 5.4 5.1 - + + -
173A GLU* 5.0 6.8 - - + +
176A PHE* 2.8 26.8 + - + -
177A PRO 3.6 20.0 - - - -
178A THR* 3.4 18.9 - - - -
179A PRO* 3.6 32.5 - - + -
182A LEU* 3.6 22.3 - - + +
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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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134A GLN* 2.9 45.7 + - - +
135A ARG* 3.8 15.1 - - - +
137A TRP* 1.3 94.8 - - + +
139A ASP* 1.3 65.7 + - - +
140A CYS 3.1 1.1 + - - -
141A HIS* 3.4 29.4 + - + +
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Residues in contact with ASP 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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87A GLU* 5.3 0.3 - - - +
89A ALA* 3.5 19.3 - - + +
90A CYS* 3.5 14.6 + - - +
92A ARG* 3.0 17.6 + - - -
93A HIS* 2.6 37.9 + - + +
135A ARG* 2.9 38.2 + - - +
136A TRP 3.2 0.8 + - - +
138A GLU* 1.3 79.8 - - - +
140A CYS* 1.3 59.2 + - - +
141A HIS 3.5 0.4 - - - -
142A THR* 4.4 8.3 + - - -
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Residues in contact with CYS 140 (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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90A CYS* 2.0 52.3 - - - -
93A HIS* 4.9 0.2 - - - -
94A PHE* 3.9 6.5 - - - -
136A TRP* 3.3 33.8 + - - +
137A TRP* 3.3 5.9 + - - +
138A GLU 3.1 1.4 - - - -
139A ASP* 1.3 77.8 - - - +
141A HIS* 1.3 63.8 + - - +
142A THR 3.2 3.4 - - - -
143A SER* 2.9 12.8 + - - -
172A PHE* 3.2 37.0 - - + +
182A LEU* 5.5 0.2 - - + -
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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
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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