Contacts of the helix formed by residues 139 - 146 (chain A) in PDB entry 3K6R
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 LEU 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU* 4.2 19.3 - - + -
116A ARG* 4.3 16.2 - - + -
119A MSE 3.7 40.1 - - + +
131A ASP* 4.5 7.2 + - - +
133A PHE 6.1 1.1 - - - +
134A ALA 5.0 0.4 + - - -
138A HIS* 1.3 85.8 - - + +
140A SER* 1.3 62.0 + - - +
142A PRO* 3.6 9.1 - - - +
143A ILE* 3.8 9.5 - - - +
197A LEU* 3.9 21.3 - - + -
199A GLY* 3.8 23.6 - - - +
222A HIS* 6.3 0.9 - - + -
224A HIS* 3.8 26.2 - - + +
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Residues in contact with SER 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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131A ASP* 2.8 28.3 + - - +
134A ALA* 4.5 0.2 - - - +
137A GLY* 3.2 8.9 + - - -
139A LEU* 1.3 78.6 - - - +
141A LEU* 1.3 64.5 + - - +
142A PRO 3.4 0.7 - - - -
143A ILE* 3.3 8.1 + - - +
144A ALA* 3.0 22.2 + - - +
151A VAL* 3.8 27.0 - - - +
153A ALA* 4.3 2.9 - - - +
177A MSE 3.4 18.9 - - - +
197A LEU* 4.0 7.6 - - - -
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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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97A ILE* 3.8 14.1 - - + -
99A TYR* 3.8 18.6 - - + -
136A ILE 3.7 10.3 - - - +
137A GLY* 2.8 29.5 + - - +
140A SER* 1.3 72.9 - - - +
142A PRO* 1.4 59.7 - - + +
144A ALA* 3.2 1.6 + - - +
145A VAL* 2.9 34.0 + - - +
167A ASN* 3.6 46.9 - - + +
168A ILE* 4.2 5.8 - - + +
171A ASN* 3.7 14.1 - - + +
173A VAL* 4.3 7.2 - - + -
177A MSE 3.8 24.9 - - + -
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Residues in contact with PRO 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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95A ASN* 6.0 0.4 - - - +
97A ILE* 3.9 18.6 - - + -
99A TYR* 3.5 18.2 - - - +
116A ARG* 3.4 29.6 - - + +
119A MSE 4.1 2.9 - - + -
120A ALA* 3.7 20.2 - - + +
138A HIS 3.5 19.1 - - - +
139A LEU 3.6 8.3 - - - +
140A SER 3.5 3.6 - - - -
141A LEU* 1.4 94.0 - - + +
143A ILE* 1.3 55.2 + - - +
146A TYR* 2.9 35.8 + - + +
147A GLY 3.6 0.3 + - - -
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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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119A MSE 3.3 29.2 - - - +
122A VAL* 4.3 11.2 - - + -
123A ALA* 4.1 7.0 - - + -
129A VAL* 3.9 23.8 - - + -
139A LEU 3.8 15.9 - - - +
140A SER* 3.3 8.0 + - - +
141A LEU 3.3 0.2 - - - -
142A PRO* 1.3 75.6 - - - +
144A ALA* 1.3 66.8 + - - +
147A GLY* 3.0 21.7 + - - +
148A LYS 3.1 7.3 + - - -
149A ALA* 3.8 10.2 + - + -
151A VAL* 3.7 20.0 - - + -
195A ARG* 4.3 4.3 - - - -
197A LEU* 3.9 30.7 - - + -
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Residues in contact with ALA 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 SER 3.0 9.6 + - - +
141A LEU 3.9 2.9 - - - +
143A ILE* 1.3 78.0 - - - +
145A VAL* 1.3 60.9 + - - +
148A LYS* 3.4 8.3 - - - -
149A ALA 4.3 6.3 - - - -
151A VAL* 4.1 12.3 - - + -
173A VAL* 3.9 20.9 - - + -
176A ARG* 3.0 31.6 + - + -
177A MSE 3.7 29.6 - - + -
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Residues in contact with VAL 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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96A GLY 5.5 3.6 - - - +
97A ILE* 3.7 26.0 - - + -
141A LEU 2.9 19.8 + - - +
142A PRO 4.4 0.2 - - - +
144A ALA* 1.3 78.6 - - - +
146A TYR* 1.3 73.9 + - + +
148A LYS* 4.4 2.9 + - - +
171A ASN* 3.9 25.6 - - + +
173A VAL* 3.8 22.9 - - + -
176A ARG* 4.3 7.0 + - - +
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Residues in contact with TYR 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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95A ASN* 2.5 50.7 + - - -
96A GLY* 4.0 4.8 - - - -
97A ILE* 3.8 21.1 - - + -
120A ALA* 3.3 32.8 - - + +
142A PRO* 2.9 16.2 + - + +
145A VAL* 1.3 82.1 - - + +
147A GLY* 1.3 65.7 + - - +
148A LYS* 3.2 4.8 + - - +
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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