Contacts of the strand formed by residues 61 - 68 (chain A) in PDB entry 1PNG
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 ARG 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASP* 3.9 21.4 + - - +
59A TRP* 3.7 36.5 - - + +
60A ASP* 1.3 78.8 - - - +
62A TYR* 1.3 64.7 + - - +
82A ILE* 3.4 4.3 - - - -
83A THR* 2.7 45.3 + - + +
117A THR* 4.0 17.0 - - + -
118A GLU* 3.0 28.6 + - - +
119A THR* 4.3 1.6 - - - -
120A TRP* 3.0 45.4 - - - +
121A LEU* 6.3 0.4 - - - +
125A ARG* 5.8 1.6 - - + +
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Residues in contact with TYR 62 (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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60A ASP 4.2 0.6 + - - -
61A ARG* 1.3 72.3 - - - +
63A ALA* 1.3 65.2 + - - +
64A ASN* 3.6 26.1 + - - -
77A GLU* 3.9 2.8 + - - -
80A ARG* 4.0 19.7 - - - -
81A PHE 3.9 4.5 - - - -
82A ILE* 4.2 16.3 - - + +
116A TYR* 4.2 6.3 - + - -
117A THR* 3.5 0.5 - - - +
118A GLU* 2.8 45.4 + - - +
152A ASN* 2.7 36.2 + - - +
153A LYS 4.2 1.6 - - - -
154A SER* 3.6 24.7 - - - -
155A SER* 3.8 21.1 - - - -
189A SER* 4.0 9.4 - - - -
294A ALA* 3.6 23.6 - - + +
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Residues in contact with ALA 63 (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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61A ARG 4.4 2.7 - - - +
62A TYR* 1.3 79.8 - - - +
64A ASN* 1.3 61.2 + - - +
80A ARG* 3.1 7.8 - - - +
81A PHE* 3.0 66.9 + - + +
83A THR* 4.7 0.2 - - + -
115A ILE* 5.8 0.4 - - + -
116A TYR 3.1 17.3 - - - +
117A THR* 3.8 14.1 - - + +
127A TYR* 4.1 2.5 - - - +
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Residues in contact with ASN 64 (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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62A TYR* 3.6 7.6 + - - -
63A ALA* 1.3 76.1 - - - +
65A VAL* 1.3 65.1 + - - +
66A TYR* 3.1 29.8 + - - -
77A GLU* 2.9 31.6 + - + +
79A GLY 3.2 10.8 - - - +
80A ARG* 3.5 2.2 - - + +
81A PHE* 4.5 1.7 - - - -
114A LYS 3.9 0.5 - - - +
115A ILE* 3.5 3.7 - - - +
116A TYR* 2.9 47.6 + - - +
152A ASN 3.1 25.1 + - - -
153A LYS 4.8 0.2 + - - -
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Residues in contact with VAL 65 (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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12A PHE* 5.3 2.9 - - + -
45A MET* 3.3 38.8 - - + -
47A ILE* 4.6 13.0 - - + -
64A ASN* 1.3 78.8 - - - +
66A TYR* 1.3 65.3 + - - +
77A GLU* 3.3 6.4 - - - +
78A ILE* 2.8 44.4 + - + -
79A GLY 2.8 13.0 + - - +
81A PHE* 4.7 2.7 - - + -
113A LEU* 4.8 8.3 - - + -
114A LYS 3.2 12.1 - - - +
115A ILE* 4.1 24.2 - - + -
129A VAL* 5.5 0.7 - - + -
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Residues in contact with TYR 66 (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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64A ASN* 3.1 41.1 + - - -
65A VAL* 1.3 81.9 - - - +
67A VAL* 1.3 60.9 + - - +
75A TRP* 3.6 37.9 - - + -
76A TYR 3.0 9.6 - - - +
77A GLU* 3.5 31.4 - - + -
78A ILE* 4.4 2.2 - - - +
113A LEU* 3.3 9.2 - - - +
114A LYS* 2.8 55.4 + - + +
116A TYR* 4.8 7.2 - + + -
150A GLN* 4.3 6.7 - - - -
152A ASN* 3.4 20.4 + - - -
153A LYS* 3.9 10.4 + - - +
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Residues in contact with VAL 67 (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 TYR* 1.3 75.3 - - - +
68A LYS* 1.3 69.1 + - - +
75A TRP* 3.6 2.2 - - - -
76A TYR* 2.9 37.1 + - + +
78A ILE* 3.5 25.5 - - + +
103A PHE* 4.5 6.7 - - + -
106A LEU* 3.8 33.9 - - + +
107A LEU* 4.0 10.8 - - + -
111A THR* 3.4 32.3 - - + -
112A GLU 3.7 3.4 - - - +
113A LEU* 4.1 5.8 - - + -
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Residues in contact with LYS 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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28A GLU* 5.5 1.2 + - - -
67A VAL* 1.3 79.1 - - - +
69A ASN* 1.3 66.2 + - - +
70A LYS* 3.2 15.5 + - + +
73A GLY* 3.6 30.1 - - - -
74A GLU 3.5 9.4 - - - +
75A TRP* 3.4 42.5 - - + +
106A LEU* 3.7 9.7 - - - +
111A THR* 5.3 1.6 - - - +
112A GLU* 2.8 50.0 + - + +
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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