Contacts of the strand formed by residues 137 - 143 (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 ASN 137 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LEU 3.5 1.0 - - - +
72C LYS* 3.1 10.2 - - - +
73C PHE* 2.8 62.0 + - + +
74C THR* 4.3 5.3 - - - +
75C VAL 4.5 0.8 - - - +
120C PRO* 3.4 18.6 - - + +
121C ASP* 3.0 12.8 + - + +
122C GLU* 2.8 50.3 + - - +
135C LYS 3.5 6.9 + - - -
136C LEU* 1.3 75.8 - - - +
138C VAL* 1.3 62.8 + - - +
139C GLU* 5.3 1.8 - - + +
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Residues in contact with VAL 138 (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* 4.1 30.7 - - + +
71C LEU 3.3 4.3 - - - +
72C LYS* 4.1 22.0 - - + -
121C ASP* 5.3 2.9 - - - +
136C LEU* 4.1 8.9 + - + +
137C ASN* 1.3 78.5 - - - +
139C GLU* 1.3 78.9 + - - +
140C GLU* 5.2 1.6 - - + +
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Residues in contact with GLU 139 (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 3.5 1.9 - - - +
70C GLU* 4.6 0.4 - - - -
71C LEU* 2.8 42.1 + - + +
73C PHE* 3.7 30.1 - - + -
118C ILE* 4.2 13.7 - - + -
119C ALA 3.6 16.1 - - - +
121C ASP* 4.1 20.4 + - - +
137C ASN* 5.3 1.4 - - + +
138C VAL* 1.3 85.1 - - - +
140C GLU* 1.3 61.0 + - - +
141C ARG* 2.8 38.7 + - - +
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Residues in contact with GLU 140 (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* 3.9 16.0 - - + -
69C ILE 3.2 17.7 - - - +
70C GLU* 4.0 16.7 - - + +
138C VAL* 4.4 2.1 - - + +
139C GLU* 1.3 74.5 + - - +
141C ARG* 1.3 85.9 + - - +
170C TYR* 2.5 39.3 + - - -
172C LYS* 5.6 0.2 + - - -
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Residues in contact with ARG 141 (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* 3.5 1.6 - - - -
69C ILE* 2.7 39.5 + - + +
71C LEU* 6.2 0.2 - - + -
94C LEU* 4.1 15.5 - - + -
115C ILE* 4.0 19.1 - - + -
116C ASP* 2.5 36.6 + - - +
117C THR 3.5 14.6 + - - -
118C ILE* 3.9 25.2 - - + +
119C ALA 4.8 2.0 - - - +
139C GLU* 2.8 41.5 + - - +
140C GLU* 1.3 90.8 + - - +
142C SER* 1.3 62.4 + - - +
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Residues in contact with SER 142 (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* 2.7 43.6 + - - -
67C ILE 3.2 14.6 - - - -
68C PHE* 3.7 20.7 - - - -
115C ILE* 4.5 7.4 - - - +
141C ARG* 1.3 77.6 - - - +
143C VAL* 1.3 69.4 + - - +
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Residues in contact with VAL 143 (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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65C GLU 3.8 0.7 - - - +
66C ARG* 3.2 10.1 - - - +
67C ILE* 3.0 41.2 + - + +
69C ILE* 3.7 16.8 - - + -
96C TYR* 3.4 45.8 - - + +
115C ILE* 3.3 33.4 - - + -
142C SER* 1.3 81.9 - - - +
144C GLY* 1.3 62.6 + - - +
146C LEU* 4.5 6.5 - - + +
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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