Contacts of the strand formed by residues 161 - 171 (chain F) in PDB entry 3HPN
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 CYS 161 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E ASN* 3.2 34.0 - - - +
42F VAL 3.3 2.9 - - - -
43F CYS* 2.1 45.1 - - - -
45F VAL* 3.8 4.3 - - + +
75F VAL* 3.3 4.9 - - - +
76F ARG* 2.8 42.6 + - + +
81F PHE* 3.8 10.1 - - + -
88F CYS* 5.1 0.4 - - - -
89F LYS 4.2 3.0 + - - -
160F ALA* 1.3 72.4 - - - +
162F VAL* 1.3 58.6 + - - +
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Residues in contact with VAL 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ASN* 3.8 2.2 - - - -
25F TRP* 4.4 14.7 - - + -
40F TYR 3.9 0.7 - - - +
41F SER* 3.4 6.3 + - - -
42F VAL* 3.0 32.7 + - + +
73F PHE* 4.2 4.7 - - + -
74F THR 3.3 11.4 - - - +
75F VAL* 4.2 7.9 - - + +
92F PHE* 3.8 45.8 - - + -
157F ASP* 4.7 4.5 - - - +
160F ALA* 3.5 28.9 - - + -
161F CYS* 1.3 74.7 - - - +
163F ALA* 1.3 69.9 + - - +
164F LEU* 3.9 2.9 - - + +
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Residues in contact with ALA 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E MET* 3.7 21.5 - - - -
33E ASN* 3.5 6.6 + - - +
39F MET* 4.2 14.4 - - - -
40F TYR 3.7 3.8 - - - -
41F SER* 4.2 6.7 - - - +
73F PHE* 3.0 3.9 - - - -
74F THR* 2.9 46.1 + - - +
162F VAL* 1.3 73.0 - - - +
164F LEU* 1.3 59.4 + - - +
165F LEU* 3.0 12.7 - - + +
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Residues in contact with LEU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 4.1 3.6 - - - -
16F TRP* 5.2 0.2 - - + -
25F TRP* 4.3 12.6 - - + -
39F MET* 3.3 4.0 - - - -
40F TYR* 2.7 45.6 + - + +
54F LEU* 4.2 16.8 - - + -
71F LEU* 4.4 11.2 - - + -
72F LYS 3.6 15.3 - - - +
73F PHE* 3.9 11.9 - - + -
92F PHE* 4.3 15.5 - - + -
155F PHE* 3.9 28.3 - - + -
162F VAL* 3.9 2.7 - - + +
163F ALA* 1.3 70.3 - - - +
165F LEU* 1.3 60.0 + - - +
166F SER 4.0 8.7 - - - +
167F VAL* 3.8 26.0 - - + -
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E MET* 4.1 9.6 - - + -
132E ARG* 2.9 47.9 + - + -
7F PHE* 3.7 8.2 - - - -
37F ILE* 4.4 14.1 - - + -
38F TYR 4.4 3.8 - - - +
39F MET* 3.3 39.9 - - + -
72F LYS 2.7 14.5 + - - +
73F PHE* 4.1 7.4 - - - -
74F THR* 4.2 15.5 - - + +
136F LEU* 4.2 9.9 - - + -
163F ALA* 3.0 39.7 - - + +
164F LEU* 1.3 73.4 - - - +
166F SER* 1.3 56.8 + - - +
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Residues in contact with SER 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU 4.8 3.7 + - - -
132E ARG* 4.5 8.5 - - - -
6F ASP* 4.9 1.9 + - - -
7F PHE* 4.1 5.8 - - - -
8F ALA* 4.1 12.0 + - - +
70F GLU* 4.2 7.0 + - - -
71F LEU* 3.6 3.6 - - - -
72F LYS* 3.0 57.7 + - - +
164F LEU* 3.6 3.3 - - - +
165F LEU* 1.3 82.6 - - - +
167F VAL* 1.3 74.7 + - - +
168F ARG* 4.7 4.9 + - - +
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Residues in contact with VAL 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 3.7 6.9 - - + +
6F ASP* 3.5 2.8 + - - -
7F PHE* 2.9 42.6 + - + +
16F TRP* 3.9 22.2 - - + -
69F ILE* 4.9 0.7 - - + -
70F GLU 3.4 3.8 - - - +
71F LEU* 3.9 17.3 - - + -
153F LEU* 4.7 6.1 - - + -
155F PHE* 4.0 12.6 - - + -
164F LEU* 3.8 28.9 - - + -
166F SER* 1.3 81.5 + - - +
168F ARG* 1.3 61.7 + - - +
169F VAL* 4.4 16.6 - - + -
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Residues in contact with ARG 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F GLU* 3.1 32.3 + - - +
3F VAL* 3.8 29.8 - - + +
5F LEU 3.4 5.8 - - - +
6F ASP* 3.7 24.5 + - - +
68F PHE 3.7 1.4 - - - +
69F ILE* 3.5 2.1 - - - +
70F GLU* 2.7 69.7 + - + +
166F SER* 4.9 4.0 - - - +
167F VAL* 1.3 76.2 - - - +
169F VAL* 1.3 63.3 + - - +
170F TYR* 3.6 23.3 - - + -
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Residues in contact with VAL 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F VAL* 3.6 2.3 - - - +
4F LEU* 2.7 32.4 + - + -
5F LEU* 2.8 37.9 + - + +
67F ILE* 3.9 31.0 - - + -
68F PHE 3.3 7.9 - - - +
69F ILE* 4.4 5.4 - - + -
151F PHE* 4.0 16.6 - - + -
153F LEU* 3.6 27.4 - - + -
167F VAL* 4.4 6.3 - - + -
168F ARG* 1.3 77.8 - - - +
170F TYR* 1.3 66.2 + - - +
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Residues in contact with TYR 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F GLU* 3.3 39.2 + - + -
2F VAL 3.1 22.2 - - - +
3F VAL* 4.0 7.6 - - + -
4F LEU* 4.3 2.2 - - - +
67F ILE* 3.4 4.8 - - - -
68F PHE* 2.6 67.4 + + + +
70F GLU* 4.7 7.2 - - + -
140F GLU* 2.6 37.3 + - - -
168F ARG* 3.6 29.8 - - - -
169F VAL* 1.3 79.5 - - - +
171F TYR* 1.3 66.1 + - - +
172F LYS* 3.8 20.5 + - + -
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Residues in contact with TYR 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F GLU* 3.7 3.1 - - - -
2F VAL* 3.0 60.6 + - + +
4F LEU* 3.9 19.5 - - + -
61F ARG 4.7 1.8 - - - -
62F GLY* 5.7 0.6 - - - -
63F GLU* 3.5 21.5 + - + +
64F ALA* 3.5 39.0 - - + -
65F GLU 5.2 0.7 - - - -
66F ARG 3.3 22.0 - - - +
67F ILE* 4.2 2.9 - - + -
68F PHE* 4.3 1.8 - - - -
170F TYR* 1.3 77.2 - - - +
172F LYS* 1.3 74.7 + - - +
173F LYS* 3.1 42.8 + - + -
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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