Contacts of the helix formed by residues 125 - 139 (chain A) in PDB entry 5ZF6
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 ASP 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A SER* 1.3 75.5 + - - +
126A LYS* 1.3 60.8 + - - +
128A ILE* 3.1 9.8 + - - +
129A LEU* 3.0 39.4 + - + +
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Residues in contact with LYS 126 (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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102A TYR* 5.3 8.1 - - + +
104A GLN* 4.2 15.7 - - + +
124A SER* 3.4 8.4 + - - +
125A ASP* 1.3 77.6 - - - +
127A GLU* 1.3 57.1 + - - +
129A LEU* 4.4 10.5 - - + -
130A THR* 2.7 49.1 + - - +
164A GLU* 3.6 30.6 + - - -
166A ASP* 4.2 16.0 + - - -
192A ARG* 6.0 0.4 - - - +
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Residues in contact with GLU 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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102A TYR* 3.2 30.6 - - + +
103A ARG* 3.8 2.1 - - - -
104A GLN* 2.9 50.7 + - + +
124A SER* 3.3 28.3 + - - +
125A ASP 3.2 0.4 - - - -
126A LYS* 1.3 78.6 - - - +
128A ILE* 1.3 60.2 + - + +
130A THR* 4.2 0.3 - - - -
131A SER* 2.6 37.4 + - - -
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Residues in contact with ILE 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 SER 3.3 17.5 - - - +
125A ASP* 3.1 11.3 + - - +
127A GLU* 1.3 79.0 - - + +
129A LEU* 1.3 71.8 + - + +
131A SER* 3.4 5.9 + - - +
132A ARG* 3.0 25.6 + - + +
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Residues in contact with LEU 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 ASP* 3.0 29.3 + - + +
126A LYS* 3.9 9.9 - - + +
128A ILE* 1.3 83.2 - - + +
130A THR* 1.3 62.4 + - - +
132A ARG* 3.2 29.2 + - - +
133A ILE* 3.0 34.5 + - + +
449A GLY* 5.1 8.3 - - - +
452A ALA* 4.6 25.6 - - + -
456A LYS* 6.3 2.9 - - + -
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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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102A TYR* 3.7 39.3 - - + -
126A LYS* 2.7 36.4 + - - +
129A LEU* 1.3 72.2 - - - +
131A SER* 1.3 63.5 + - - +
133A ILE* 3.2 10.1 + - + +
134A ILE* 3.0 36.7 + - + +
166A ASP* 3.7 34.3 + - + +
170A ILE* 5.7 0.9 - - + -
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Residues in contact with SER 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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100A VAL* 3.4 35.7 + - - +
101A ASP* 4.5 0.3 + - - -
102A TYR* 3.3 21.3 + - - +
127A GLU* 2.6 24.9 + - - +
128A ILE* 3.7 5.8 - - - +
129A LEU 3.3 0.2 - - - -
130A THR* 1.3 77.4 - - - +
132A ARG* 1.3 57.8 + - - +
134A ILE* 3.4 3.5 + - - +
135A ASP* 3.0 27.1 + - - +
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Residues in contact with ARG 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 ILE* 3.0 18.7 + - + +
129A LEU* 3.7 31.8 + - - +
130A THR 3.2 0.2 - - - -
131A SER* 1.3 75.3 - - - +
133A ILE* 1.3 65.9 + - - +
135A ASP* 2.9 23.6 + - + +
136A ARG* 2.9 61.7 + - + +
230A GLU* 3.6 23.8 + - - +
449A GLY* 4.5 17.6 + - - -
452A ALA* 6.2 0.2 - - - +
558A GLN* 3.6 18.2 + - - +
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Residues in contact with ILE 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 LEU* 3.0 25.7 + - + +
130A THR* 3.2 8.2 + - + +
132A ARG* 1.3 80.8 - - - +
134A ILE* 1.3 56.2 + - - +
136A ARG* 3.6 22.1 + - - +
137A SER* 2.6 33.3 + - - -
170A ILE* 3.6 25.4 - - + -
192A ARG* 6.3 0.4 - - - +
217A VAL* 4.3 12.6 - - + -
228A MET* 3.8 21.6 - - + +
230A GLU* 4.1 24.7 - - + +
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Residues in contact with ILE 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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100A VAL* 3.8 23.6 - - + -
102A TYR* 4.2 3.6 - - + -
130A THR* 3.0 27.6 + - + +
131A SER 3.7 4.9 - - - +
133A ILE* 1.3 76.3 - - - +
135A ASP* 1.3 63.4 + - - +
137A SER* 3.2 15.2 + - - -
138A ILE* 3.3 15.4 + - + +
152A VAL* 4.9 0.7 - - + -
154A CYS* 3.8 15.3 - - - -
169A ALA* 3.7 29.8 - - + -
170A ILE* 3.7 24.9 - - + +
173A ALA* 3.7 28.5 - - + -
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Residues in contact with ASP 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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98A LEU* 3.9 13.9 - - - +
99A VAL* 5.1 0.2 - - - -
100A VAL* 4.4 13.0 + - + +
131A SER 3.0 13.4 + - - +
132A ARG* 2.9 16.8 + - + +
134A ILE* 1.3 77.4 - - - +
136A ARG* 1.3 60.9 + - + +
137A SER 3.2 0.2 + - - -
138A ILE* 3.2 5.9 + - - -
139A ARG* 2.6 79.2 + - - +
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Residues in contact with ARG 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 ARG* 2.9 64.8 + - + +
133A ILE* 3.9 9.6 - - - +
134A ILE 3.4 0.2 - - - -
135A ASP* 1.3 78.6 - - + +
137A SER* 1.3 57.7 + - - +
138A ILE 3.4 0.2 - - - -
139A ARG* 4.8 1.3 - - - +
140A PRO* 3.2 26.4 - - - +
227A VAL 3.9 11.8 - - - +
228A MET* 3.7 24.8 - - + +
229A LEU 3.4 16.0 + - - -
230A GLU* 3.2 25.5 - - - +
558A GLN* 4.0 6.4 - - - +
559A ALA 3.5 13.3 + - - -
560A ASP* 2.9 29.6 + - - +
561A ILE 5.1 1.5 - - - +
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Residues in contact with SER 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 ILE 2.6 22.4 + - - -
134A ILE 3.2 6.2 + - - -
135A ASP 3.1 1.0 - - - -
136A ARG* 1.3 77.9 - - - +
138A ILE* 1.3 61.4 + - - +
140A PRO* 4.4 1.3 - - - -
141A LEU* 4.6 2.8 - - - +
170A ILE* 3.7 23.3 - - - +
184A TRP* 4.3 0.2 - - - -
188A VAL* 3.7 23.7 - - - +
219A ALA* 3.6 10.8 - - - +
227A VAL* 3.8 9.8 - - - +
228A MET* 3.5 27.2 - - - +
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Residues in contact with ILE 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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98A LEU* 4.3 15.5 - - + -
100A VAL* 4.1 16.2 - - + -
134A ILE* 3.3 16.4 + - + +
135A ASP* 3.7 4.3 - - - +
137A SER* 1.3 85.1 - - - +
139A ARG* 1.3 67.6 + - - +
140A PRO* 3.4 3.4 - - - -
141A LEU* 3.4 5.9 + - - -
142A PHE* 3.4 5.2 - - + -
152A VAL* 4.0 20.4 - - + -
170A ILE* 5.1 3.1 - - + +
173A ALA* 4.2 23.1 - - + -
174A SER* 4.7 2.0 - - - +
177A LEU* 3.9 19.5 - - + -
184A TRP* 2.8 51.8 + - + +
188A VAL* 5.5 1.6 - - + -
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Residues in contact with ARG 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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96A MET* 3.8 40.3 + - + +
98A LEU* 2.9 36.5 + - + +
135A ASP* 2.6 59.1 + - - +
136A ARG* 4.8 1.8 - - - +
138A ILE* 1.3 74.2 - - - +
140A PRO* 1.3 67.5 - - + +
141A LEU 3.0 1.6 + - - -
142A PHE* 3.4 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