Contacts of the helix formed by residues 136 - 145 (chain A) in PDB entry 4P4P
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 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A SER 4.8 4.3 - - - +
135A LEU* 1.3 76.5 - - - +
137A ASP* 1.3 65.5 + - - +
138A GLN* 3.7 8.2 + - - +
139A GLN* 2.8 45.3 + - - +
140A ARG* 3.0 22.8 + - - +
10B T 5.4 0.9 - - - -
11B G 4.2 31.0 - - - -
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Residues in contact with ASP 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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135A LEU 5.0 0.9 - - - +
136A THR* 1.3 73.5 - - - +
138A GLN* 1.3 60.7 + - - +
140A ARG* 3.2 16.3 + - - +
141A VAL* 3.0 29.0 + - + +
234A THR 5.6 1.8 - - - +
11B G 4.4 12.9 + - - +
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Residues in contact with GLN 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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103A HIS* 2.8 37.9 + - + +
104A GLY* 5.0 6.5 - - - -
136A THR* 3.2 9.6 + - - +
137A ASP* 1.3 77.8 - - - +
139A GLN* 1.3 59.0 + - + +
141A VAL* 3.2 9.5 + - - +
142A GLY* 3.0 23.6 + - - -
234A THR 5.1 0.4 - - - -
235A MET* 3.2 38.1 + - + +
236A ALA* 4.3 4.2 - - - +
243A MET* 4.1 11.6 - - - +
9B C 5.8 1.0 + - - -
10B T 4.1 21.0 + - - +
11B G 5.2 2.1 + - - +
3C G 5.9 2.0 - - - +
5C A 4.7 5.2 - - - +
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Residues in contact with GLN 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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103A HIS 3.9 7.0 - - - -
104A GLY* 2.9 32.6 + - - +
105A PHE* 3.4 28.3 - - + -
109A ALA* 3.7 23.4 - - - +
134A SER 4.5 0.9 - - - +
135A LEU* 3.5 12.9 - - + +
136A THR* 2.8 48.6 + - - +
138A GLN* 1.3 75.8 - - + +
140A ARG* 1.3 58.4 + - - +
142A GLY* 3.1 2.4 + - - -
143A ILE* 2.9 34.1 + - - +
4C T 5.4 1.4 - - - -
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Residues in contact with ARG 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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129A ALA* 3.1 31.1 + - + +
130A ASP* 4.1 14.4 + - - +
132A ILE 2.9 21.9 + - - -
133A PRO* 3.2 25.5 + - - +
135A LEU* 3.5 28.7 + - + +
136A THR 3.0 16.0 + - - +
137A ASP* 3.2 16.6 + - - +
139A GLN* 1.3 75.7 - - - +
141A VAL* 1.3 58.8 + - + +
143A ILE* 3.8 7.3 - - + +
144A LYS* 2.9 31.0 + - - +
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Residues in contact with VAL 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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137A ASP* 3.0 17.0 + - + +
138A GLN* 3.2 8.5 + - - +
140A ARG* 1.3 75.2 - - + +
142A GLY* 1.3 65.9 + - - +
144A LYS* 4.5 3.1 - - + +
145A TYR* 2.9 45.0 + - + +
233A ALA* 4.1 19.1 - - + -
234A THR 3.8 19.5 - - - +
235A MET* 3.8 27.6 - - + -
245A MET* 4.3 2.9 - - + -
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Residues in contact with GLY 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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102A VAL* 4.1 9.5 - - - +
103A HIS* 3.7 31.5 + - - -
138A GLN 3.0 11.3 + - - -
139A GLN 3.1 4.4 + - - -
141A VAL* 1.3 77.5 - - - +
143A ILE* 1.3 60.0 - - - +
145A TYR 3.8 0.9 - - - -
146A PHE* 3.2 24.6 + - - +
149A ILE* 3.9 9.2 - - - +
235A MET* 4.2 1.8 - - - -
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Residues in contact with ILE 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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102A VAL* 3.8 18.4 - - + -
105A PHE* 3.6 18.6 - - + -
125A LEU* 4.2 12.6 - - + -
126A LEU* 3.9 26.0 - - + +
129A ALA* 3.8 24.5 - - + -
135A LEU* 3.7 26.7 - - + -
139A GLN 2.9 22.1 + - - +
140A ARG* 3.8 7.0 - - - +
142A GLY* 1.3 77.1 - - - +
144A LYS* 1.3 69.0 + - + +
146A PHE* 3.1 20.0 + - - +
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Residues in contact with LYS 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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140A ARG 2.9 18.6 + - - +
141A VAL* 4.1 3.4 - - - +
143A ILE* 1.3 80.4 - - + +
145A TYR* 1.3 92.6 + - + +
146A PHE 3.3 0.9 + - - -
147A TYR 5.1 0.7 + - - -
148A ASP* 4.8 2.8 - - - +
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Residues in contact with TYR 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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141A VAL* 2.9 31.6 + - + +
142A GLY 3.8 2.5 - - - -
144A LYS* 1.3 112.5 + - + +
146A PHE* 1.3 65.3 + - - +
147A TYR 3.3 2.7 - - - -
148A ASP* 3.2 21.2 + - - -
149A ILE* 2.9 35.8 + - + +
232A GLU* 2.4 42.2 + - + +
233A ALA* 3.5 26.1 - - + +
245A MET* 3.9 20.6 - - + -
247A ARG* 4.4 4.3 - - - -
267A ALA* 3.8 13.7 - - + -
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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