Contacts of the strand formed by residues 166 - 173 (chain D) in PDB entry 3HN3
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 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D GLU* 3.3 3.2 - - - -
105D VAL* 2.7 45.1 + - + +
107D LEU* 3.9 33.8 - - + +
134D VAL* 3.2 35.7 - - + -
135D ASN* 3.6 9.4 - - - +
153D ILE* 3.9 24.7 - - + -
156D LEU 5.8 0.2 - - - +
157D VAL* 4.5 7.6 - - + -
165D ARG* 1.3 71.8 - - - +
167D ARG* 1.3 63.3 + - - +
168D ILE* 4.0 21.3 - - + -
220D LEU* 4.1 13.0 - - + -
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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
----------------------------------------------------------
64D TYR* 2.9 29.5 + - - +
65D ARG 3.3 18.2 + - - -
66D ARG* 3.1 16.1 + - - +
67D PRO* 4.0 16.3 - - - +
102D GLU* 3.0 45.0 + - + +
103D ARG 3.6 2.7 - - - -
104D GLU* 4.0 25.4 - - + +
133D TRP 3.7 1.6 - - - +
134D VAL* 3.5 4.3 - - - -
135D ASN* 2.8 47.6 + - - +
136D GLY* 3.5 19.3 - - - +
165D ARG 3.7 1.3 + - - +
166D LEU* 1.3 73.3 - - - +
168D ILE* 1.3 61.4 + - - +
169D THR* 3.2 11.8 + - - +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 3.6 31.0 - - + -
45D TRP* 4.0 11.5 - - + -
101D TYR 3.9 0.2 - - - +
102D GLU* 3.2 5.6 - - - +
103D ARG* 2.8 36.7 + - + +
105D VAL* 4.1 11.7 - - + -
121D LEU* 3.8 36.6 - - + -
132D VAL* 4.2 5.4 - - + -
133D TRP 3.6 3.1 - - - +
134D VAL* 4.9 2.7 - - + -
166D LEU* 4.0 23.8 - - + -
167D ARG* 1.3 73.6 - - - +
169D THR* 1.3 62.5 + - - +
170D ILE* 3.9 25.1 - - + -
220D LEU* 4.6 0.4 - - + -
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Residues in contact with THR 169 (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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64D TYR* 4.5 8.5 - - + -
68D LEU* 5.3 5.4 - - + -
100D TRP* 4.1 26.7 - - + -
101D TYR 3.4 11.2 - - - +
102D GLU* 2.9 26.7 + - + +
132D VAL* 3.3 3.6 - - - +
133D TRP* 2.7 59.7 + - + +
136D GLY 5.4 0.3 + - - -
167D ARG* 3.2 16.3 + - - +
168D ILE* 1.3 72.3 - - - +
170D ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 170 (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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45D TRP* 4.0 25.1 - - + -
99D VAL 3.7 1.2 - - - +
100D TRP* 3.6 1.7 - - - -
101D TYR* 2.8 46.4 + - + +
123D ILE* 3.6 33.0 - - + -
126D ALA* 5.7 0.2 - - + -
130D ALA* 4.6 6.1 - - + -
131D ILE 3.4 9.2 - - - +
132D VAL* 4.1 15.0 - - + -
133D TRP* 4.5 0.9 - - - -
149D PHE* 5.7 2.2 - - + -
168D ILE* 3.9 12.6 - - + -
169D THR* 1.3 80.5 - - - +
171D ALA* 1.3 62.0 + - - +
172D ILE* 3.8 25.7 + - + -
214D LEU* 4.1 15.0 - - + -
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Residues in contact with ALA 171 (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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59D PHE* 4.3 0.4 - - + -
98D TRP* 3.6 22.6 - - + -
99D VAL 3.3 5.2 - - - +
100D TRP* 4.0 22.7 - - + +
130D ALA* 3.2 4.7 - - - +
131D ILE* 2.9 31.3 + - + +
133D TRP* 3.6 28.3 - - + -
170D ILE* 1.3 72.6 - - - +
172D ILE* 1.3 60.6 + - - +
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Residues in contact with ILE 172 (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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97D GLY 3.5 1.6 - - - +
98D TRP* 3.3 5.4 - - - -
99D VAL* 2.9 44.3 + - + +
101D TYR* 4.0 13.0 - - + -
126D ALA* 4.3 4.7 - - + -
127D HIS* 3.5 34.3 - - + +
129D TYR 3.3 6.7 - - - +
130D ALA* 4.3 6.7 - - + -
170D ILE* 3.8 13.0 - - + +
171D ALA* 1.3 78.5 - - - +
173D ASN* 1.3 62.5 + - - +
174D ASN* 4.1 1.1 + - + +
212D ALA* 5.4 2.7 - - + -
213D GLY* 3.9 21.5 - - - +
214D LEU* 3.7 37.2 - - + -
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Residues in contact with ASN 173 (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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97D GLY 3.3 5.8 + - - -
98D TRP* 3.1 33.7 - - + +
127D HIS* 3.6 2.6 - - - +
128D SER* 3.1 23.9 + - - -
129D TYR* 2.7 17.4 + - + +
172D ILE* 1.3 73.9 - - - +
174D ASN* 1.3 60.1 + - - +
175D THR* 2.9 32.1 + - - +
1G NAG 1.4 71.8 + - - +
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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