Contacts of the strand formed by residues 160 - 167 (chain D) in PDB entry 4H0N
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 ARG 160 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLU* 4.1 23.7 + - + +
118D ASN 3.4 17.7 - - - +
119D VAL* 4.3 12.6 - - - +
120D LYS* 4.5 4.0 - - - +
146D LEU* 3.3 7.2 - - - -
147D LEU 3.0 30.6 + - - -
158D ARG* 3.4 62.5 - - + +
159D LEU* 1.3 90.8 + - - +
161D TYR* 1.3 61.9 + - - +
162D TYR* 3.4 26.4 - - + +
231D CYS* 4.1 12.5 - - - -
232D PHE 5.1 0.8 + - - -
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Residues in contact with TYR 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D MET* 4.2 8.5 - - + -
117D GLU* 3.7 1.2 - - - +
118D ASN* 3.0 46.9 + - + +
119D VAL 3.5 23.1 - - - +
120D LYS 4.2 0.2 - - - +
122D PHE* 3.4 28.3 - + - -
123D GLU* 3.5 32.8 - - + +
128D ARG* 4.2 0.6 - - + +
131D PHE* 4.4 1.2 - - - -
132D ILE* 4.0 8.0 - - - +
144D GLU* 2.7 34.5 + - + -
145D PHE 3.3 9.4 - - - -
146D LEU* 3.6 12.7 - - + +
160D ARG* 1.3 73.9 - - - +
162D TYR* 1.3 90.7 + - - +
163D CYS* 3.4 19.9 - - + +
180D ILE* 5.5 0.7 - - + -
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Residues in contact with TYR 162 (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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15D MET* 6.2 0.2 - - + -
115D LEU* 4.7 12.8 - - + -
116D MET 3.4 14.4 - - - -
117D GLU* 3.3 32.1 + - + +
144D GLU* 3.2 5.0 - - - -
145D PHE* 2.6 48.6 + - + +
147D LEU* 4.0 35.0 + - + -
149D PRO* 6.0 1.4 - - - +
158D ARG 5.4 0.7 + - - -
160D ARG* 3.4 39.0 - - + +
161D TYR* 1.3 85.2 - - - +
163D CYS* 1.3 63.1 + - - +
164D THR* 6.0 1.8 - - + -
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Residues in contact with CYS 163 (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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114D ILE* 3.8 1.0 - - - +
115D LEU* 3.4 4.4 - - - +
116D MET* 2.9 36.5 + - + +
131D PHE* 3.7 29.8 - - + -
132D ILE* 4.6 1.1 - - - -
135D LEU* 4.2 3.1 - - - -
142D TYR* 4.1 21.1 - - - -
143D GLN 3.3 11.4 - - - +
144D GLU* 4.5 4.9 - - + -
145D PHE* 4.8 0.2 - - - -
161D TYR* 3.4 22.2 - - + +
162D TYR* 1.3 79.1 - - - +
164D THR* 1.3 68.6 + - - +
165D ALA* 4.5 2.0 - - - -
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Residues in contact with THR 164 (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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114D ILE 3.5 5.2 - - - -
115D LEU* 4.0 25.8 - - + -
142D TYR* 3.1 2.4 - - - -
143D GLN* 2.8 38.9 + - - +
145D PHE* 3.3 28.4 - - + -
162D TYR* 6.0 1.6 - - + -
163D CYS* 1.3 77.4 - - - +
165D ALA* 1.3 58.9 + - - +
172D TRP* 3.8 19.5 - - - -
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Residues in contact with ALA 165 (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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112D ASP 3.9 0.2 - - - +
113D TYR* 3.7 0.5 - - - +
114D ILE* 2.8 43.4 + - + +
131D PHE* 5.5 0.2 - - + -
135D LEU* 3.9 29.6 - - + -
140D PHE* 3.9 10.2 - - + -
141D ILE 3.2 10.1 - - - +
142D TYR* 3.9 9.2 - - + -
163D CYS* 4.0 4.0 - - - -
164D THR* 1.3 74.2 - - - +
166D ARG* 1.3 67.3 + - - +
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Residues in contact with ARG 166 (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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112D ASP 3.2 11.3 + - - +
113D TYR* 3.7 39.9 + - + -
140D PHE* 3.3 6.3 - - - -
141D ILE* 2.7 42.1 + - + +
164D THR* 6.6 0.2 - - - -
165D ALA* 1.3 78.8 - - - +
167D ARG* 1.3 66.7 + - - +
169D ASN* 4.8 0.4 + - - -
171D THR* 2.7 40.4 + - - -
172D TRP* 3.2 62.8 - - + +
173D PRO* 4.7 1.8 - - - +
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Residues in contact with ARG 167 (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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105D LEU* 6.0 0.2 - - - +
108D LEU* 4.1 4.4 + - - +
109D ASP* 3.1 40.7 + - - +
111D VAL* 2.7 24.6 + - - +
112D ASP* 3.0 40.7 + - + +
138D CYS* 2.8 27.7 + - - +
139D ASN* 3.8 17.2 - - - +
140D PHE* 3.5 21.9 - - - -
141D ILE* 4.7 2.8 - - - +
166D ARG* 1.3 78.0 + - - +
168D ASN* 1.3 53.8 + - - +
169D ASN* 2.8 48.7 + - + +
170D LEU 4.7 0.2 + - - -
171D THR* 4.8 0.5 + - - -
172D TRP* 5.6 1.9 - - - +
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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