Contacts of the strand formed by residues 67 - 75 (chain C) 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 ILE 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.2 16.8 - - + -
64C ALA* 4.0 18.6 - - + -
66C ARG* 1.3 79.0 - - - +
68C PHE* 1.3 61.6 + - - +
69C ILE* 4.2 17.6 - - + +
96C TYR* 6.3 1.3 - - + -
142C SER* 3.2 7.6 - - - -
143C VAL* 3.0 40.4 + - + +
146C LEU* 3.5 29.2 - - + -
151C PHE* 3.5 32.8 - - + -
153C LEU* 4.4 2.5 - - + -
169C VAL* 3.8 13.7 - - + -
170C TYR 3.5 7.0 - - - +
171C TYR* 4.4 2.2 - - + -
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ARG* 4.2 30.3 - - + -
67C ILE* 1.3 75.5 - - - +
69C ILE* 1.3 60.8 + - - +
70C GLU 4.1 0.7 - - - -
140C GLU* 3.9 17.9 - - + -
141C ARG 3.5 2.2 - - - -
142C SER* 3.7 20.6 - - - -
169C VAL* 3.2 5.9 - - - +
170C TYR* 2.6 77.1 + + + +
171C TYR* 4.3 0.9 - - - -
172C LYS* 3.7 36.1 - - + -
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Residues in contact with ILE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ILE* 4.2 12.6 - - + +
68C PHE* 1.3 78.3 - - - +
70C GLU* 1.3 60.6 + - - +
71C LEU* 4.0 24.6 - - + +
94C LEU* 4.4 14.8 - - + -
115C ILE* 4.1 8.3 - - + -
139C GLU 3.5 2.1 - - - +
140C GLU* 3.2 6.4 - - - +
141C ARG 2.7 43.0 + - - +
143C VAL* 3.7 29.6 - - + -
153C LEU* 3.8 46.2 - - + -
167C VAL* 4.9 0.9 - - + -
168C ARG 3.5 6.1 - - - +
169C VAL* 4.4 3.8 - - + -
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Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C PHE 4.1 0.4 - - - -
69C ILE* 1.3 72.3 - - - +
71C LEU* 1.4 64.2 + - - +
72C LYS* 3.7 27.4 + - + +
138C VAL* 4.1 21.0 - - + +
139C GLU 3.7 2.9 - - - +
140C GLU* 4.0 21.7 - - + +
166C SER* 3.8 4.9 + - - +
167C VAL* 3.4 5.9 - - - -
168C ARG* 2.6 73.6 + - + +
170C TYR* 4.7 4.0 - - + -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 4.0 13.7 - - + +
70C GLU* 1.4 80.6 - - - +
72C LYS* 1.3 63.7 + - - +
73C PHE* 3.9 12.6 - - + -
92C PHE* 4.0 20.9 - - + -
94C LEU* 4.5 9.2 - - + -
118C ILE* 4.1 22.7 - - + -
137C ASN 3.5 1.0 - - - +
138C VAL* 3.3 5.0 - - - +
139C GLU* 2.8 44.7 + - + +
141C ARG* 6.2 0.4 - - + -
155C PHE* 3.7 33.9 - - + -
164C LEU* 4.4 4.9 - - + -
166C SER 3.5 1.1 - - - +
167C VAL* 4.0 22.7 - - + -
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 3.7 28.3 + - + +
71C LEU* 1.3 77.0 - - - +
73C PHE* 1.3 58.8 + - - +
136C LEU* 4.1 16.8 - - + +
137C ASN 3.1 9.2 - - - +
138C VAL* 4.1 21.5 - - + +
164C LEU* 3.5 3.8 - - - +
165C LEU* 2.8 30.8 + - + -
166C SER* 3.0 35.7 + - - +
131D ALA* 2.6 40.5 + - - +
132D ARG* 4.2 6.1 - - + -
133D HIS* 5.4 5.1 - - - -
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Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LEU* 3.9 11.0 - - + -
72C LYS* 1.3 79.4 - - - +
74C THR* 1.3 63.3 + - - +
75C VAL* 3.6 26.5 - - + -
92C PHE* 3.5 27.6 - + + -
118C ILE* 3.5 26.7 - - + -
119C ALA 3.9 8.3 - - - -
120C PRO* 3.9 14.8 - - + -
136C LEU* 3.7 4.3 - - - +
137C ASN* 2.8 59.3 + - + +
139C GLU* 3.7 25.4 - - + -
162C VAL* 4.2 4.9 - - + -
163C ALA 3.0 16.6 - - - +
164C LEU* 4.0 10.5 - - + -
165C LEU* 4.1 2.2 - - - -
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Residues in contact with THR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C PHE* 1.3 75.9 - - - +
75C VAL* 1.3 66.1 + - - +
124C THR* 4.4 2.7 - - - -
134C VAL* 3.7 22.0 - - + -
135C LYS 3.3 24.9 - - - +
136C LEU* 4.3 6.7 - - + -
137C ASN* 4.3 1.1 - - - +
162C VAL* 3.3 5.2 - - - +
163C ALA* 2.9 34.4 + - - +
165C LEU* 4.2 13.0 - - + -
32D MET* 3.9 4.3 - - + -
33D ASN* 2.9 28.1 + - - -
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C PHE* 3.6 23.8 - - + -
74C THR* 1.3 81.5 - - - +
76C ARG* 1.3 71.7 - - - +
89C LYS 4.7 2.5 - - - +
90C GLU* 3.9 34.5 - - + +
92C PHE* 5.1 2.7 - - + -
120C PRO* 3.7 27.4 - - + -
122C GLU 5.1 0.4 + - - -
123C ILE* 3.8 4.8 - - + -
124C THR* 2.9 28.7 + - - -
135C LYS 4.8 0.6 + - - -
137C ASN* 4.5 4.0 - - - +
160C ALA* 4.9 2.7 - - + -
161C CYS 3.4 10.5 - - - +
162C VAL* 4.5 10.1 - - + -
33D ASN* 4.4 1.1 - - - -
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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