Contacts of the strand formed by residues 149 - 155 (chain D) in PDB entry 3C6M
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 ASN 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ASP* 3.2 21.2 + - - -
143D GLU 3.3 7.0 + - - -
144D ASP* 3.0 29.1 + - - +
148D GLN* 1.3 77.2 - - - +
150D ILE* 1.3 64.9 + - - +
151D LYS* 3.2 37.9 + - - +
163D ILE 3.9 0.9 - - - +
164D LEU* 3.5 5.5 - - - -
165D SER* 3.0 36.1 + - - +
166D GLY 5.2 4.0 + - - -
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TYR* 3.6 24.0 - - + -
142D ASP* 3.4 3.8 - - - -
143D GLU 2.9 37.7 + - - +
145D SER* 4.0 6.5 - - - +
148D GLN* 3.8 16.6 - - + +
149D ASN* 1.3 78.0 - - - +
151D LYS* 1.3 63.3 + - - +
152D ILE* 5.0 1.3 - - + -
162D LEU* 3.9 15.7 - - + -
163D ILE 4.0 1.6 - - - -
164D LEU* 3.8 16.2 - - + -
222D ASP* 3.7 12.6 - - - +
224D MET* 3.9 13.9 - - + +
225D VAL* 3.6 40.2 - - + +
228D GLY* 6.2 0.7 - - - -
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Residues in contact with LYS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG* 5.7 7.7 - - - +
121D ASP* 5.7 2.0 - - + -
124D TRP* 3.6 37.5 - - + -
139D VAL* 5.7 0.4 - - + -
141D TYR 3.3 4.5 - - - +
142D ASP* 3.3 33.3 + - - +
149D ASN* 3.2 26.6 + - - +
150D ILE* 1.3 72.8 - - - +
152D ILE* 1.3 67.0 + - - +
153D LEU* 4.1 17.9 - - + -
161D ILE 4.1 0.2 - - - -
162D LEU* 3.4 2.1 - - - +
163D ILE* 2.8 51.6 + - + +
166D GLY* 5.8 2.2 - - - +
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 2.8 33.7 + - + +
141D TYR* 2.8 32.0 + - + +
150D ILE* 5.3 0.7 - - + -
151D LYS* 1.3 78.3 - - - +
153D LEU* 1.3 63.8 + - - +
160D ASN* 3.9 32.3 - - + -
161D ILE 3.3 4.7 - - - +
162D LEU* 3.8 26.0 - - + -
228D GLY* 3.6 34.5 - - - +
232D TYR* 4.1 15.7 - - + -
233D MET* 4.2 11.9 - - + -
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP* 3.5 16.6 - - + +
124D TRP* 3.5 39.3 - - + +
136D ILE* 3.7 23.8 - - + -
138D GLU 3.4 2.7 - - - -
139D VAL* 3.6 36.3 - - + -
151D LYS* 4.2 18.6 - - + -
152D ILE* 1.3 83.5 - - - +
154D HIS* 1.3 61.4 + - - +
155D SER 3.6 0.5 + - - -
160D ASN* 4.0 2.5 - - - -
161D ILE* 2.7 43.0 + - + +
163D ILE* 3.9 14.1 - - + -
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Residues in contact with HIS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LEU* 4.0 13.8 - - + +
330B GLU* 2.9 38.3 + - - -
334B ARG* 5.0 0.6 + - - -
136D ILE* 3.2 5.7 - - - -
137D ASP* 2.7 58.0 + - - +
138D GLU* 2.9 22.2 + - + +
140D VAL* 3.8 11.8 - - + +
153D LEU* 1.3 71.7 - - - +
155D SER* 1.3 76.1 + - - +
156D LYS* 3.6 20.4 - - - -
159D GLY* 4.0 4.1 - - - -
160D ASN* 3.3 24.0 + - - +
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Residues in contact with SER 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D TYR* 5.5 0.2 - - - -
135D ASP* 2.7 30.9 + - - -
136D ILE* 4.0 4.5 - - - -
153D LEU 3.6 0.8 + - - -
154D HIS* 1.3 85.2 - - - +
156D LYS* 1.3 59.6 + - - +
158D PHE* 2.9 25.4 + - - -
159D GLY 2.8 38.3 + - - -
161D ILE* 3.7 22.9 - - - -
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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