Contacts of the strand formed by residues 117 - 124 (chain D) in PDB entry 3D87
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 117 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 3.8 18.7 - - - +
112D LYS 4.4 2.1 + - - -
113D ASN* 4.3 9.0 + - - +
115D SER* 3.1 20.6 + - - +
116D GLY 1.3 81.8 + - - +
118D PHE* 1.3 60.9 + - - +
147D THR 4.4 3.6 + - - -
149D GLY 6.0 0.2 - - - +
170D GLU* 2.7 49.6 + - - +
171D CYS* 3.1 7.5 - - - +
172D GLN* 3.0 55.3 + - - +
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Residues in contact with PHE 118 (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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109D CYS* 4.7 0.9 - - + -
110D GLU 3.2 19.3 - - - +
111D ALA* 4.3 5.6 - - + +
116D GLY 3.6 14.6 - - - -
117D ARG* 1.3 75.4 - - - +
119D THR* 1.3 64.4 + - - +
120D CYS* 3.5 24.7 - - - -
136D SER* 3.6 21.5 - - - -
146D VAL* 4.0 9.6 - - + -
169D VAL 3.4 1.0 - - - +
170D GLU* 3.5 3.1 - - - +
171D CYS* 2.8 59.8 + - + +
173D GLU* 5.2 2.5 - - + -
186D ILE* 3.7 24.2 - - + -
188D VAL* 3.9 4.7 - - + -
205D PHE* 3.5 23.3 - + - -
207D ILE* 4.1 10.8 - - + -
210D ILE* 4.5 6.5 - - + -
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Residues in contact with THR 119 (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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109D CYS* 2.9 22.9 - - - +
110D GLU 2.9 12.8 + - - -
118D PHE* 1.3 72.4 + - - +
120D CYS* 1.3 67.9 + - - +
121D TRP* 3.0 37.5 - - + -
168D SER* 3.9 15.5 - - - -
169D VAL 3.1 6.9 + - - +
170D GLU* 2.4 37.6 + - - +
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Residues in contact with CYS 120 (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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107D LEU* 5.3 3.4 - - + -
108D ARG 2.8 19.1 - - - +
109D CYS* 3.1 26.0 - - - -
118D PHE* 3.5 26.7 - - - -
119D THR* 1.3 79.6 - - - +
121D TRP* 1.3 66.1 + - - +
122D TRP* 3.7 16.5 - - + -
167D TYR 3.7 0.2 - - - +
168D SER* 2.7 23.3 - - - -
169D VAL* 3.0 13.8 + - + +
171D CYS* 5.4 2.2 - - - -
188D VAL* 4.5 11.2 - - + -
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Residues in contact with TRP 121 (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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98D GLN* 5.0 1.9 - - - +
106D PHE 3.8 0.2 - - - +
107D LEU* 3.6 4.0 - - - -
108D ARG* 2.9 83.2 + - + +
109D CYS* 3.8 2.5 - - - -
110D GLU* 3.7 31.4 - - + -
119D THR* 3.0 45.3 - - + -
120D CYS* 1.3 79.8 - - - +
122D TRP* 1.3 70.8 + - - +
123D LEU* 5.5 1.6 - - + -
154D SER* 5.1 0.2 + - - -
166D GLU* 3.3 32.8 + - + +
167D TYR 2.8 8.5 - - - +
168D SER* 3.6 16.6 + - - -
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Residues in contact with TRP 122 (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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95D LEU* 3.0 44.2 - - + -
98D GLN* 4.9 2.9 - - - -
106D PHE 3.5 6.3 - - - +
107D LEU* 3.7 16.4 - - + -
120D CYS* 3.7 12.6 - - + -
121D TRP* 1.3 87.6 - - - +
123D LEU* 1.3 71.4 + - - +
124D THR* 4.9 1.1 - - + -
132D PHE* 3.5 23.0 - + + -
134D VAL* 3.8 20.6 - - + -
151D ALA* 3.4 25.6 - - + -
165D TYR 3.5 0.9 - - - +
166D GLU* 3.3 16.3 - - - +
167D TYR* 3.0 49.5 + + + +
169D VAL* 3.0 36.1 - - + -
188D VAL* 5.8 1.3 - - + -
190D VAL* 4.1 7.6 - - + -
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Residues in contact with LEU 123 (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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95D LEU* 3.1 10.4 - - + +
96D LYS* 2.3 65.7 + - + +
98D GLN* 4.5 18.4 + - + +
106D PHE 4.5 0.2 + - - -
121D TRP* 5.5 1.8 - - + -
122D TRP* 1.3 84.0 - - - +
124D THR* 1.3 52.8 - - - +
157D ARG* 5.0 10.5 - - + +
164D GLU* 3.1 42.2 - - + +
165D TYR 3.6 4.5 - - - +
166D GLU* 3.3 32.8 - - + +
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Residues in contact with THR 124 (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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94D ILE 3.3 18.0 + - - -
95D LEU* 4.5 2.5 - - - +
96D LYS* 4.3 0.4 - - - +
122D TRP* 4.9 0.4 - - + -
123D LEU* 1.3 74.6 - - - +
125D THR* 1.3 60.7 + - - +
126D ILE* 2.7 33.0 + - - +
130D LEU* 3.9 6.6 - - + +
132D PHE* 4.7 5.8 - - + -
164D GLU* 3.9 2.7 - - - -
165D TYR* 2.8 40.5 + - + +
167D TYR* 3.1 37.9 - - + +
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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