Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 3I5Y
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU* 1.3 75.6 - - - +
131A PRO* 1.3 71.9 - - + +
132A VAL* 3.3 1.4 - - - +
133A GLN* 3.0 31.7 + - - +
134A GLN* 2.8 27.1 + - - +
156A THR* 2.8 34.8 + - - +
1000A ANP 3.3 36.8 - - + +
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Residues in contact with PRO 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 LEU 4.7 0.4 - - - +
130A THR* 1.3 88.7 - - + +
132A VAL* 1.3 62.1 + - - +
134A GLN* 3.4 11.8 + - + +
135A LYS* 3.0 25.8 + - - +
156A THR* 5.2 8.7 - - + +
330A THR* 4.0 17.8 - - + +
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Residues in contact with VAL 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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130A THR* 3.3 0.9 - - - +
131A PRO* 1.3 79.0 - - - +
133A GLN* 1.3 64.9 + - - +
135A LYS* 3.3 1.1 + - - -
136A THR* 3.0 47.5 + - + +
150A ALA* 4.8 5.2 - - + -
151A ARG 5.2 0.4 - - - +
152A ALA* 3.4 34.7 - - + +
156A THR* 3.3 28.9 - - - +
157A GLY 4.3 1.3 - - - -
158A LYS* 4.1 15.5 - - + +
161A ALA* 4.1 11.0 - - + -
304A PHE* 4.2 10.8 - - + -
328A LEU 6.0 0.4 - - - +
330A THR* 3.6 12.5 - - + +
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Residues in contact with GLN 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* 3.5 17.7 - - + +
130A THR* 3.0 26.4 + - - +
132A VAL* 1.3 78.7 - - - +
134A GLN* 1.3 61.7 + - - +
136A THR* 4.1 4.3 - - - -
137A ILE* 3.1 42.2 + - + +
157A GLY* 3.0 27.0 + - - +
160A PHE* 3.6 17.6 - - - +
161A ALA* 3.8 14.4 - - - +
164A ILE* 5.2 1.3 - - - -
1000A ANP 2.8 50.8 + - - -
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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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100A LYS 4.4 0.7 - - - +
101A GLU* 3.3 23.8 + - - +
102A VAL* 2.6 72.5 + - + +
107A LEU* 6.0 0.8 - - - +
129A LEU* 2.9 32.6 + - + +
130A THR 2.8 22.2 + - - +
131A PRO* 3.7 9.8 - - + +
133A GLN* 1.3 73.2 - - - +
135A LYS* 1.3 61.2 + - - +
137A ILE* 4.4 3.5 + - - +
138A LYS* 5.1 4.9 + - - +
139A PRO* 5.4 1.2 - - - +
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Residues in contact with LYS 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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93A VAL* 3.2 30.1 + - - +
94A PRO 2.9 25.3 + - - -
95A LYS* 3.7 5.5 - - - +
96A GLU* 4.3 4.4 - - - +
131A PRO 3.0 18.7 + - - +
132A VAL* 3.8 5.8 - - - +
133A GLN 3.2 0.2 - - - -
134A GLN* 1.3 78.4 - - - +
136A THR* 1.3 60.1 + - + +
139A PRO* 3.4 22.2 - - - +
328A LEU* 3.4 16.9 - - + +
329A ASP 2.9 32.5 + - - +
330A THR* 4.2 11.2 - - + +
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Residues in contact with THR 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 VAL* 3.0 37.2 + - + +
133A GLN 3.9 1.9 + - - -
135A LYS* 1.3 81.9 - - + +
137A ILE* 1.3 62.0 + - - +
138A LYS 3.4 2.2 + - - -
139A PRO* 3.5 1.9 - - - +
140A ILE* 2.9 48.5 + - - +
148A VAL* 5.3 0.2 - - + -
150A ALA* 4.0 17.5 - - + -
161A ALA* 3.3 23.0 + - - +
304A PHE* 4.3 2.2 - - + -
328A LEU* 3.7 23.1 - - + +
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Residues in contact with ILE 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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104A LEU* 6.1 0.2 - - + -
107A LEU* 4.1 15.5 - - + -
112A VAL* 4.5 1.6 - - + -
113A LEU* 3.8 28.0 - - + -
129A LEU* 4.3 18.4 - - + -
133A GLN* 3.1 29.2 + - + +
134A GLN 4.4 1.7 + - - +
135A LYS 3.8 0.2 - - - -
136A THR* 1.3 76.5 + - - +
138A LYS* 1.3 63.7 + - - +
140A ILE* 3.6 1.7 + - - +
141A LEU* 3.3 28.8 + - + +
160A PHE 5.0 0.2 - - - +
161A ALA* 4.4 6.5 - - - +
164A ILE* 4.0 33.0 - - + -
165A PRO* 4.0 23.7 - - + +
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Residues in contact with LYS 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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107A LEU* 4.7 10.2 - - + +
110A GLU* 3.0 29.1 + - - +
112A VAL* 4.3 27.8 - - + -
134A GLN 5.1 4.0 + - - +
137A ILE* 1.3 76.3 - - - +
139A PRO* 1.3 71.4 - - + +
141A LEU* 3.1 4.9 + - - +
142A SER* 2.8 30.1 + - - -
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Residues in contact with PRO 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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134A GLN 5.4 0.7 - - - +
135A LYS 3.4 22.4 - - - +
136A THR 3.6 7.9 - - - +
138A LYS* 1.3 97.3 - - + +
140A ILE* 1.3 63.1 + - - +
142A SER* 3.0 14.4 + - - -
146A HIS* 3.0 25.6 - - - +
148A VAL* 4.8 1.8 - - + -
326A LEU* 3.8 26.0 - - + -
328A LEU* 3.9 14.4 - - + -
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Residues in contact with ILE 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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136A THR* 2.9 37.9 + - - +
137A ILE 3.9 3.8 - - - +
139A PRO* 1.3 71.8 - - - +
141A LEU* 1.3 58.7 + - - +
142A SER 4.2 2.8 - - - +
146A HIS* 4.8 2.4 - - - -
148A VAL* 4.2 28.0 - - + +
161A ALA 3.4 26.0 - - - +
162A PHE* 4.7 0.4 - - - -
165A PRO* 3.6 23.3 - - + -
166A ILE* 6.1 0.9 - - + -
263A TYR* 3.0 33.0 + - + -
300A LYS* 5.0 3.6 - - - +
302A LEU* 3.8 27.6 - - + -
304A PHE* 4.1 15.9 - - + -
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Residues in contact with LEU 141 (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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112A VAL* 3.9 23.6 - - + +
113A LEU* 4.3 6.3 - - + -
137A ILE* 3.3 16.9 + - + +
138A LYS 3.1 5.1 + - - +
140A ILE* 1.3 74.8 - - - +
142A SER* 1.3 66.8 + - - +
143A SER* 3.4 3.3 + - - -
165A PRO* 3.2 34.3 - - + +
168A GLN* 3.5 35.7 - - + -
169A HIS* 3.9 17.9 - - + +
172A ASN* 4.6 8.2 + - - +
263A TYR* 4.2 9.5 + - + +
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Residues in contact with SER 142 (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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138A LYS* 2.8 16.2 + - - -
139A PRO* 3.0 21.1 + - - +
140A ILE 4.2 0.7 - - - +
141A LEU* 1.3 77.5 - - - +
143A SER* 1.3 59.3 + - - +
144A GLU* 3.1 34.8 + - - +
146A HIS* 3.9 10.3 - - - -
300A LYS* 3.2 18.4 + - - -
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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