Contacts of the strand formed by residues 67 - 75 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.1 16.2 - - + -
64A ALA* 4.0 21.1 - - + -
65A GLU 4.1 0.2 - - - -
66A ARG* 1.3 77.0 - - - +
68A PHE* 1.3 63.1 + - - +
69A ILE* 4.3 16.3 - - + +
96A TYR* 6.2 1.6 - - + -
142A SER* 3.2 7.3 - - - -
143A VAL* 3.0 40.9 + - + +
146A LEU* 3.6 28.3 - - + -
151A PHE* 3.5 33.4 - - + -
153A LEU* 4.4 2.5 - - + -
169A VAL* 3.9 13.5 - - + -
170A TYR 3.5 6.5 - - - +
171A TYR* 4.5 1.8 - - + -
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 4.1 30.7 - - + -
67A ILE* 1.3 75.2 - - - +
69A ILE* 1.3 61.8 + - - +
70A GLU 4.1 0.2 - - - -
140A GLU* 3.9 18.8 - - + -
141A ARG 3.6 2.0 - - - -
142A SER* 3.6 22.4 - - - -
169A VAL* 3.2 6.8 - - - +
170A TYR* 2.6 72.3 + + + +
171A TYR* 4.4 0.7 - - - -
172A LYS* 3.6 42.6 - - + -
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 4.3 13.0 - - + +
68A PHE* 1.3 79.4 - - - +
70A GLU* 1.3 60.9 + - - +
71A LEU* 3.9 25.7 - - + +
94A LEU* 4.3 15.3 - - + -
115A ILE* 4.1 9.4 - - + -
139A GLU 3.7 2.1 - - - +
140A GLU* 3.2 6.8 - - - +
141A ARG* 2.7 41.7 + - - +
143A VAL* 3.8 27.8 - - + -
153A LEU* 3.9 44.0 - - + -
167A VAL* 4.9 0.9 - - + -
168A ARG 3.5 5.4 - - - +
169A VAL* 4.4 3.8 - - + -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE 4.1 0.4 - - - -
69A ILE* 1.3 71.5 - - - +
71A LEU* 1.3 66.2 + - - +
72A LYS* 3.8 24.8 + - + +
138A VAL* 4.0 22.7 - - + +
139A GLU 3.6 4.3 - - - +
140A GLU* 4.0 21.8 - - + +
166A SER* 3.7 5.9 + - - +
167A VAL* 3.4 5.9 - - - -
168A ARG* 2.7 69.9 + - + +
170A TYR* 4.7 4.2 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 3.9 14.1 - - + +
70A GLU* 1.3 84.0 - - - +
72A LYS* 1.3 62.5 + - - +
73A PHE* 3.9 14.4 - - + -
92A PHE* 4.1 10.1 - - + -
94A LEU* 4.5 11.2 - - + -
118A ILE* 4.1 31.0 - - + -
137A ASN 3.5 0.7 - - - +
138A VAL* 3.3 5.2 - - - +
139A GLU* 2.8 41.4 + - + +
141A ARG* 6.1 0.7 - - + -
155A PHE* 3.8 33.4 - - + -
164A LEU* 4.3 4.0 - - + -
166A SER 3.5 1.6 - - - +
167A VAL* 3.9 22.7 - - + -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 3.8 26.5 + - - +
71A LEU* 1.3 78.0 - - - +
73A PHE* 1.3 58.2 + - - +
136A LEU* 4.1 22.9 - - + +
137A ASN 3.1 6.3 - - - +
138A VAL* 4.0 27.6 - - + -
164A LEU* 3.6 1.9 - - - +
165A LEU* 2.7 31.5 + - + -
166A SER* 3.0 36.7 + - - +
131B ALA* 2.6 38.9 + - - +
132B ARG* 4.4 2.0 + - + -
133B HIS* 5.4 5.3 - - - -
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.9 11.2 - - + -
72A LYS* 1.3 79.2 - - - +
74A THR* 1.3 62.5 + - - +
75A VAL* 3.6 26.2 - - + -
92A PHE* 3.5 26.5 - + - -
118A ILE* 3.5 28.0 - - + -
119A ALA 4.0 7.9 - - - -
120A PRO* 3.9 10.3 - - + -
136A LEU* 3.8 4.3 - - - +
137A ASN* 2.8 59.1 + - + +
139A GLU* 3.7 24.9 - - + -
162A VAL* 4.2 4.3 - - + -
163A ALA 3.0 16.2 - - - +
164A LEU* 4.0 11.9 - - + -
165A LEU* 4.2 2.7 - - - -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 1.3 75.4 - - - +
75A VAL* 1.3 67.4 - - - +
76A ARG 4.2 0.2 - - - -
124A THR* 4.5 2.5 - - - -
134A VAL* 3.7 22.0 - - + -
135A LYS 3.2 24.7 - - - +
136A LEU* 4.3 6.1 - - + -
137A ASN* 4.4 0.9 - - - +
162A VAL* 3.3 6.4 - - - +
163A ALA* 3.0 33.2 + - - +
165A LEU* 4.1 13.9 - - + -
32B MET* 3.9 4.2 - - + -
33B ASN* 2.8 28.5 + - - +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.6 28.0 - - + -
74A THR* 1.3 81.3 - - - +
76A ARG* 1.3 71.5 + - - +
77A ASP 3.6 0.2 + - - -
89A LYS 4.8 2.2 - - - +
90A GLU* 3.9 36.8 - - + +
92A PHE* 4.9 3.4 - - + -
120A PRO* 3.8 22.2 - - + -
122A GLU 4.9 0.2 + - - -
123A ILE* 3.7 6.0 - - + -
124A THR* 2.9 28.6 + - - -
135A LYS 4.7 1.0 + - - -
137A ASN* 4.5 4.8 - - - +
160A ALA* 5.0 2.0 - - + -
161A CYS 3.4 7.9 - - - +
162A VAL* 4.3 11.7 - - + -
33B ASN* 4.6 0.4 - - - -
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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