Contacts of the helix formed by residues 141 - 155 (chain A) in PDB entry 1J75
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 PRO 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A VAL* 5.1 3.1 - - + -
140A VAL* 1.3 96.0 - - + +
142A LYS* 1.3 65.7 + - - +
143A LYS* 4.4 7.2 - - + +
144A THR* 3.2 20.1 + - + +
145A LEU* 3.1 19.2 + - - +
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Residues in contact with LYS 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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131A ILE* 3.4 31.0 - - + -
135A VAL* 4.3 15.6 - - + +
140A VAL 3.9 0.2 + - - -
141A PRO* 1.3 73.2 - - - +
143A LYS* 1.3 59.2 + - - +
145A LEU* 3.1 8.2 + - - +
146A ASN* 2.8 33.3 + - - +
203B C 5.8 0.9 - - - +
204B G 3.5 15.5 - - - +
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Residues in contact with LYS 143 (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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141A PRO* 3.3 5.1 - - + +
142A LYS* 1.3 78.4 - - - +
144A THR* 1.3 65.7 + - - +
146A ASN* 3.2 2.1 + - - +
147A GLN* 3.0 40.3 + - - +
204B G 3.2 37.8 + - - +
205B C 3.8 19.0 + - - +
206B G 5.2 7.4 + - - -
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Residues in contact with THR 144 (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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114A LEU* 3.6 21.8 - - + -
140A VAL* 4.4 9.9 - - + -
141A PRO* 3.2 29.2 + - + +
143A LYS* 1.3 80.1 - - - +
145A LEU* 1.3 63.3 + - - +
147A GLN* 3.5 24.4 + - - +
148A VAL* 3.6 15.9 + - + +
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Residues in contact with LEU 145 (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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114A LEU* 3.9 8.5 - - + -
118A ILE* 3.8 28.9 - - + +
131A ILE* 3.6 18.6 - - + -
134A LEU* 3.6 17.0 - - + -
135A VAL* 3.5 40.4 - - + +
138A CYS* 4.0 8.1 - - + -
140A VAL* 3.5 27.8 - - + +
141A PRO 3.1 7.6 + - - +
142A LYS 3.1 7.5 + - - +
144A THR* 1.3 75.6 - - - +
146A ASN* 1.3 59.3 + - - +
148A VAL* 3.1 5.5 + - - +
149A LEU* 2.8 34.2 + - + +
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Residues in contact with ASN 146 (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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131A ILE* 3.7 9.4 - - - +
142A LYS* 2.8 24.5 + - - +
143A LYS 3.2 0.4 + - - +
145A LEU* 1.3 75.3 - - - +
147A GLN* 1.3 66.7 + - - +
149A LEU* 3.7 18.7 - - - +
150A TYR* 2.9 46.8 + - + +
164A ALA* 5.9 0.2 - - - -
166A TRP* 4.0 4.2 + - - -
203B C 4.0 20.1 + - - -
204B G 2.7 49.0 + - - +
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Residues in contact with GLN 147 (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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143A LYS* 3.0 31.5 + - + +
144A THR* 3.6 24.2 + - - +
145A LEU 3.2 0.4 - - - -
146A ASN* 1.3 77.6 - - - +
148A VAL* 1.3 63.3 + - + +
150A TYR* 4.4 1.4 - - - +
151A ARG* 3.4 19.6 + - - +
204B G 3.4 24.0 - - - +
205B C 2.8 21.7 + - - +
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Residues in contact with VAL 148 (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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114A LEU* 3.8 22.7 - - + -
115A GLU* 4.1 13.5 - - + +
118A ILE* 3.7 21.3 - - + -
144A THR* 3.6 14.1 + - + +
145A LEU 3.1 5.5 + - - +
147A GLN* 1.3 76.6 - - + +
149A LEU* 1.3 54.9 + - - +
151A ARG* 3.0 29.8 + - - +
152A LEU* 2.8 47.3 + - + +
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Residues in contact with LEU 149 (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 ILE* 3.9 30.1 - - + -
122A LEU* 4.5 5.2 - - + -
131A ILE* 3.7 15.5 - - + -
134A LEU* 4.0 9.6 - - + -
145A LEU* 2.8 23.7 + - + +
146A ASN* 3.7 15.9 - - - +
148A VAL* 1.3 72.2 - - - +
150A TYR* 1.3 58.0 + - - +
152A LEU* 3.2 5.5 + - + -
153A LYS* 2.8 29.1 + - - +
158A VAL* 3.6 10.8 - - + +
166A TRP* 3.5 63.3 - - + +
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Residues in contact with TYR 150 (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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146A ASN* 2.9 37.1 + - + +
147A GLN 4.5 1.3 - - - +
149A LEU* 1.3 70.4 - - - +
151A ARG* 1.3 66.1 + - - +
153A LYS* 3.4 19.3 + - + +
154A LYS* 3.1 22.7 + - - +
160A SER* 5.3 2.3 + - - -
164A ALA 5.2 1.6 + - - -
166A TRP* 3.5 28.4 - + - -
202B G 3.6 5.4 + - - +
203B C 2.4 38.2 + - - -
204B G 3.5 44.3 + + + +
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Residues in contact with ARG 151 (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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115A GLU* 3.0 34.1 + - - +
147A GLN 3.4 13.0 + - - +
148A VAL* 3.0 30.8 + - - +
150A TYR* 1.3 76.1 - - - +
152A LEU* 1.3 70.5 + - - +
154A LYS* 2.9 21.6 + - + +
155A GLU* 2.9 49.7 + - + +
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Residues in contact with LEU 152 (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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115A GLU* 3.7 32.3 - - + +
118A ILE* 4.2 14.8 - - + -
119A LEU* 4.1 21.8 - - + -
148A VAL* 2.8 40.4 + - + +
149A LEU* 3.6 2.9 - - - +
151A ARG* 1.3 76.1 - - - +
153A LYS* 1.3 60.5 + - - +
155A GLU* 3.0 22.2 + - - +
157A ARG* 2.9 46.9 + - + +
158A VAL* 3.6 24.0 - - + -
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Residues in contact with LYS 153 (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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149A LEU 2.8 15.7 + - - +
150A TYR* 3.7 18.6 - - + +
151A ARG 3.1 0.2 - - - -
152A LEU* 1.3 78.1 - - - +
154A LYS* 1.3 59.7 + - - +
156A ASP* 2.9 24.4 + - - +
158A VAL* 3.5 19.4 - - + +
159A SER* 5.2 0.4 - - - -
160A SER* 4.6 17.0 - - - +
166A TRP* 4.0 26.5 - - + -
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Residues in contact with LYS 154 (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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150A TYR 3.1 12.3 + - - +
151A ARG* 2.9 14.7 + - + +
153A LYS* 1.3 79.7 - - - +
155A GLU* 1.3 60.2 + - + +
156A ASP* 3.2 5.2 + - - +
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Residues in contact with GLU 155 (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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115A GLU* 5.4 0.2 - - - +
151A ARG* 2.9 53.6 + - + +
152A LEU* 3.0 12.1 + - - +
153A LYS 3.0 0.8 - - - -
154A LYS* 1.3 80.9 - - + +
156A ASP* 1.3 68.3 + - - +
157A ARG* 3.1 32.6 + - + +
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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