Contacts of the strand formed by residues 67 - 75 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E LEU* 4.1 15.9 - - + -
64E ALA* 4.0 19.7 - - + -
66E ARG* 1.3 77.7 - - - +
68E PHE* 1.3 61.9 + - - +
69E ILE* 4.4 16.4 - - + -
96E TYR* 6.3 1.3 - - + -
142E SER* 3.2 7.8 - - - -
143E VAL* 3.0 41.5 + - + +
146E LEU* 3.7 28.7 - - + -
151E PHE* 3.5 33.0 - - + -
153E LEU* 4.5 2.5 - - + -
169E VAL* 3.9 12.3 - - + -
170E TYR 3.4 6.5 - - - +
171E TYR* 4.4 2.5 - - + -
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Residues in contact with PHE 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ARG* 4.3 27.8 - - + -
67E ILE* 1.3 77.0 - - - +
69E ILE* 1.3 61.1 + - - +
70E GLU 4.1 0.4 - - - -
140E GLU* 3.9 17.9 - - - -
141E ARG 3.6 2.7 - - - -
142E SER* 3.8 20.4 - - - -
168E ARG 3.6 1.2 - - - +
169E VAL* 3.2 6.8 - - - +
170E TYR* 2.6 76.2 + + + +
171E TYR* 4.3 0.9 - - - -
172E LYS* 3.7 37.0 - - + -
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Residues in contact with ILE 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ILE* 4.4 13.0 - - + +
68E PHE* 1.3 78.7 - - - +
70E GLU* 1.3 61.7 + - - +
71E LEU* 3.9 24.2 + - + +
94E LEU* 4.3 15.3 - - + -
115E ILE* 4.1 9.6 - - + -
139E GLU 3.6 1.7 - - - +
140E GLU* 3.2 7.2 - - - +
141E ARG* 2.7 40.5 + - - +
143E VAL* 3.8 28.3 - - + -
153E LEU* 3.9 43.7 - - + -
167E VAL* 4.9 0.7 - - + -
168E ARG 3.5 4.5 - - - +
169E VAL* 4.5 4.3 - - + -
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Residues in contact with GLU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE 4.1 0.2 - - - -
69E ILE* 1.3 74.4 - - - +
71E LEU* 1.3 65.8 + - - +
72E LYS* 3.7 25.5 + - + +
138E VAL* 4.0 22.1 - - + +
139E GLU 3.6 3.1 - - - +
140E GLU* 3.9 21.5 - - + +
166E SER* 3.6 4.7 + - - +
167E VAL* 3.4 4.9 - - - -
168E ARG* 2.7 72.1 + - + +
170E TYR* 4.7 3.5 - - + -
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ILE* 3.9 12.8 - - + +
70E GLU* 1.3 82.2 - - - +
72E LYS* 1.3 63.9 + - - +
73E PHE* 3.9 14.2 - - + -
92E PHE* 4.2 10.1 - - + -
94E LEU* 4.5 10.1 - - + -
118E ILE* 4.1 32.5 - - + -
137E ASN 3.5 0.7 - - - +
138E VAL* 3.3 5.2 - - - +
139E GLU* 2.9 43.3 + - + +
141E ARG* 6.2 0.4 - - + -
155E PHE* 3.8 33.0 - - + -
164E LEU* 4.2 4.7 - - + -
166E SER 3.4 1.8 - - - +
167E VAL* 3.9 22.7 - - + -
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Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E GLU* 3.7 26.8 + - + +
71E LEU* 1.3 77.6 - - - +
73E PHE* 1.3 58.1 - - - +
136E LEU* 4.0 26.1 - - + +
137E ASN 3.1 5.8 - - - +
138E VAL* 4.0 23.9 - - + +
164E LEU* 3.5 3.8 - - - +
165E LEU* 2.7 31.3 + - + -
166E SER* 2.9 33.9 + - - +
130F GLU 5.2 0.9 + - - +
131F ALA* 2.8 35.7 + - - +
132F ARG* 4.3 3.6 - - + -
133F HIS* 5.9 1.8 - - - -
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Residues in contact with PHE 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 3.9 9.4 - - + -
72E LYS* 1.3 79.2 - - - +
74E THR* 1.3 64.1 + - - +
75E VAL* 3.6 27.1 - - + -
92E PHE* 3.6 23.6 - + + -
118E ILE* 3.5 22.7 - - + -
119E ALA* 4.0 7.2 - - - -
120E PRO* 3.9 16.4 - - + -
136E LEU* 3.7 4.3 - - - +
137E ASN* 2.8 55.1 + - + -
139E GLU* 3.6 31.9 - - + -
162E VAL* 4.2 5.2 - - + -
163E ALA 3.0 15.7 - - - +
164E LEU* 4.1 10.8 - - + -
165E LEU* 4.1 2.2 - - - -
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Residues in contact with THR 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E PHE* 1.3 75.9 - - - +
75E VAL* 1.3 66.8 + - - +
124E THR* 4.4 2.2 - - - -
134E VAL* 3.8 20.6 - - + -
135E LYS 3.3 25.6 - - - +
136E LEU* 4.3 6.5 - - + -
137E ASN* 4.3 0.9 - - - +
162E VAL* 3.2 8.3 - - - +
163E ALA* 2.9 34.3 + - - +
165E LEU* 4.2 13.5 - - + -
32F MET* 4.1 4.7 - - + -
33F ASN* 2.6 31.0 + - - +
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Residues in contact with VAL 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E PHE* 3.6 23.6 - - + -
74E THR* 1.3 81.5 - - - +
76E ARG* 1.3 72.5 + - - +
89E LYS 4.7 2.2 - - - +
90E GLU* 3.9 34.3 - - + +
92E PHE* 5.0 2.9 - - + -
120E PRO* 3.7 27.6 - - + -
122E GLU 5.0 0.4 + - - -
123E ILE* 3.7 5.7 - - + -
124E THR* 2.9 28.9 + - - -
137E ASN* 4.4 4.0 - - - +
160E ALA* 5.0 1.8 - - + -
161E CYS 3.3 10.3 - - - +
162E VAL* 4.4 10.5 - - + -
33F ASN* 4.2 2.0 - - - -
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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