Contacts of the strand formed by residues 161 - 171 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C ASN* 3.0 37.7 - - - +
41D SER* 6.2 0.2 - - - -
42D VAL 3.3 3.6 - - - -
43D CYS* 2.1 46.2 - - - -
45D VAL* 3.7 4.6 - - + +
75D VAL* 3.4 4.2 - - - +
76D ARG* 2.9 42.6 + - + +
81D PHE* 3.9 10.5 - - + -
88D CYS* 5.1 0.4 - - - -
89D LYS 4.2 2.4 + - - -
160D ALA* 1.3 72.0 - - - +
162D VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 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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33C ASN* 4.0 2.5 - - - -
25D TRP* 4.3 18.1 - - + -
40D TYR 3.9 0.7 - - - +
41D SER* 3.4 6.2 + - - -
42D VAL* 2.9 34.1 + - + +
73D PHE* 4.2 5.2 - - + -
74D THR 3.3 10.5 - - - +
75D VAL* 4.3 7.0 - - + -
91D THR 5.3 0.2 - - - -
92D PHE* 3.9 43.1 - - + -
157D ASP* 4.8 1.6 - - - +
160D ALA* 3.5 28.7 - - + +
161D CYS* 1.3 74.1 - - - +
163D ALA* 1.3 71.4 + - - +
164D LEU* 4.0 2.9 - - - +
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Residues in contact with ALA 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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32C MET* 3.7 21.8 - - - -
33C ASN* 3.8 4.6 + - - +
39D MET* 4.2 10.3 - - - -
40D TYR 3.6 3.8 - - - -
41D SER* 4.1 10.5 - - - +
73D PHE* 3.0 6.4 - - - -
74D THR* 2.9 49.8 + - - +
162D VAL* 1.3 75.9 - - - +
164D LEU* 1.3 60.0 - - - +
165D LEU* 3.1 10.7 - - + +
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Residues in contact with LEU 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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7D PHE* 4.0 4.4 - - + -
16D TRP* 5.2 0.4 - - + -
25D TRP* 4.3 12.1 - - + -
39D MET* 3.4 4.1 - - - -
40D TYR* 2.7 42.7 + - + +
54D LEU* 4.2 15.5 - - + -
71D LEU* 4.3 11.0 - - + -
72D LYS 3.6 14.8 - - - +
73D PHE* 4.0 11.7 - - + -
92D PHE* 4.3 15.9 - - + -
155D PHE* 3.9 30.3 - - + -
162D VAL* 4.0 1.9 - - + -
163D ALA* 1.3 72.0 - - - +
165D LEU* 1.3 59.2 + - - +
166D SER 4.1 8.1 - - - +
167D VAL* 3.8 26.0 - - + -
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Residues in contact with LEU 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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32C MET* 4.5 7.9 - - + -
132C ARG* 2.6 51.1 + - + +
7D PHE* 3.7 6.4 - - - -
8D ALA* 4.2 0.3 - - - +
37D ILE* 4.4 14.4 - - + -
38D TYR 4.2 4.5 - - - +
39D MET* 3.3 39.7 - - + -
72D LYS 2.8 12.4 + - - +
73D PHE* 4.2 7.2 - - - -
74D THR* 4.2 14.6 - - + +
136D LEU* 4.3 8.1 - - + -
163D ALA* 3.1 39.7 - - + +
164D LEU* 1.3 75.3 - - - +
166D SER* 1.3 60.3 + - - +
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Residues in contact with SER 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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130C GLU 4.4 4.0 + - - -
132C ARG* 4.2 8.5 - - - -
6D ASP* 5.0 2.3 + - - -
7D PHE* 4.1 5.8 - - - -
8D ALA* 4.1 12.4 - - - +
70D GLU* 4.2 6.5 + - - -
71D LEU* 3.4 3.8 - - - -
72D LYS* 2.9 56.3 + - - +
164D LEU* 3.5 2.2 - - - +
165D LEU* 1.3 84.4 - - - +
167D VAL* 1.3 74.0 + - - +
168D ARG* 4.8 4.3 + - - +
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Residues in contact with VAL 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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5D LEU* 3.7 7.4 - - + +
6D ASP* 3.4 3.6 + - - -
7D PHE* 2.9 45.2 + - + +
16D TRP* 4.1 18.8 - - + -
56D THR* 5.2 0.2 - - + -
69D ILE* 4.9 0.7 - - + -
70D GLU 3.4 2.9 - - - -
71D LEU* 3.9 18.6 - - + -
153D LEU* 4.6 5.6 - - + -
155D PHE* 4.0 15.7 - - + -
164D LEU* 3.8 28.9 - - + -
166D SER* 1.3 81.3 + - - +
168D ARG* 1.3 61.1 + - - +
169D VAL* 4.4 17.3 - - + -
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Residues in contact with ARG 168 (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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1D GLU* 3.1 31.5 + - - +
3D VAL* 3.8 30.1 - - + +
5D LEU 3.4 5.8 - - - +
6D ASP* 3.8 25.0 + - - +
68D PHE 3.6 1.2 - - - +
69D ILE* 3.5 1.7 - - - -
70D GLU* 2.7 68.9 + - + +
166D SER* 4.9 4.9 - - - +
167D VAL* 1.3 75.3 - - - +
169D VAL* 1.3 63.5 + - - +
170D TYR* 3.6 24.2 + - + -
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Residues in contact with VAL 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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3D VAL* 3.6 2.2 - - - +
4D LEU* 2.8 30.1 + - + -
5D LEU* 2.8 39.7 + - + +
67D ILE* 3.8 32.1 - - + -
68D PHE 3.2 8.7 - - - +
69D ILE* 4.4 5.6 - - + -
151D PHE* 4.0 15.7 - - + -
153D LEU* 3.6 27.6 - - + -
167D VAL* 4.4 6.1 - - + -
168D ARG* 1.3 77.4 - - - +
170D TYR* 1.3 64.4 + - - +
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Residues in contact with TYR 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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1D GLU* 3.3 38.7 + - + -
2D VAL 3.0 23.6 - - - +
3D VAL* 4.1 9.4 - - + -
4D LEU* 4.3 1.8 - - - +
67D ILE* 3.4 6.3 - - - +
68D PHE* 2.6 67.3 + + + +
70D GLU* 4.7 3.6 - - + -
140D GLU* 2.5 36.2 + - - -
168D ARG* 3.6 32.3 - - - -
169D VAL* 1.3 77.9 - - - +
171D TYR* 1.3 64.3 + - - +
172D LYS* 3.7 21.4 + - + -
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Residues in contact with TYR 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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1D GLU* 3.7 3.6 - - - -
2D VAL* 3.0 58.8 + - + +
4D LEU* 3.9 22.2 - - + -
61D ARG 4.6 2.2 - - - -
62D GLY* 5.7 0.7 - - - -
63D GLU* 3.7 16.5 + - + +
64D ALA* 3.4 42.1 + - + -
65D GLU 5.2 0.7 - - - -
66D ARG 3.2 23.3 - - - +
67D ILE* 4.2 2.0 - - + -
68D PHE* 4.4 2.2 - - - -
170D TYR* 1.3 77.9 - - - +
172D LYS* 1.3 74.8 + - - +
173D LYS* 3.2 43.8 + - + -
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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