Contacts of the strand formed by residues 74 - 83 (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 GLU 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LYS* 3.5 1.3 - - - -
69A ASN* 2.8 33.3 + - - +
72A THR* 3.2 26.9 + - - +
73A GLY* 1.3 77.7 - - - +
75A TRP* 1.3 67.9 + - - +
76A TYR* 3.8 19.1 + - + -
147A PRO* 3.6 20.9 - - - +
150A GLN* 4.1 6.7 + - - +
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Residues in contact with TRP 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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28A GLU* 3.8 23.0 + - + -
66A TYR* 3.6 33.4 - - + -
67A VAL 3.7 2.0 - - - -
68A LYS* 3.4 55.8 - - + +
73A GLY 5.0 2.2 - - - -
74A GLU* 1.3 78.2 - - - +
76A TYR* 1.3 61.4 + - - +
112A GLU* 3.4 33.0 - - + -
113A LEU 3.8 12.1 - - - -
114A LYS* 3.5 50.1 - - + +
150A GLN* 3.0 21.1 + - - +
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Residues in contact with TYR 76 (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* 3.0 6.2 - - - -
67A VAL* 2.9 43.8 + - + +
69A ASN* 3.6 28.3 + - + -
72A THR* 4.4 5.5 + - - +
74A GLU* 3.9 26.1 + - + -
75A TRP* 1.3 81.3 - - - +
77A GLU* 1.3 62.2 + - - +
78A ILE* 3.3 2.8 + - - +
103A PHE* 4.3 11.7 - + + -
106A LEU* 4.0 29.2 - - + -
145A VAL* 3.8 23.1 + - + -
146A VAL* 4.3 6.7 - - - +
147A PRO* 3.4 27.9 - - + +
150A GLN* 3.9 9.6 - - - +
298A PHE* 3.8 18.8 - + + -
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Residues in contact with GLU 77 (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* 3.9 0.9 + - - -
64A ASN* 2.9 30.1 + - + +
65A VAL 3.3 10.1 - - - +
66A TYR* 3.5 10.8 - - + -
76A TYR* 1.3 68.7 - - - +
78A ILE* 1.3 62.3 + - - +
79A GLY* 3.9 13.0 - - - +
80A ARG* 3.1 35.7 + - - +
103A PHE* 3.7 3.5 - - - -
150A GLN* 3.1 9.4 + - - +
152A ASN* 3.0 30.0 + - - +
185A ARG* 5.3 0.7 + - - -
187A THR* 4.5 2.9 - - - +
296A SER* 2.8 26.9 + - - +
298A PHE* 3.3 21.4 - - - -
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Residues in contact with ILE 78 (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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45A MET* 4.0 16.2 - - + -
65A VAL* 2.8 37.3 + - + +
66A TYR 4.7 1.3 - - - +
67A VAL* 3.5 39.5 - - + +
76A TYR 3.6 5.8 - - - +
77A GLU* 1.3 74.8 - - - +
79A GLY* 1.3 58.8 + - - +
98A ILE* 4.0 1.6 - - - +
100A VAL* 3.7 21.4 - - + +
103A PHE* 3.7 32.8 - - + -
107A LEU* 5.0 7.2 - - + -
113A LEU* 5.1 1.8 - - + -
131A PHE* 4.5 11.7 - - + -
185A ARG* 3.0 27.0 + - - -
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Residues in contact with GLY 79 (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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45A MET* 5.6 1.8 - - - -
64A ASN* 3.2 5.5 - - - +
65A VAL* 2.8 34.4 + - - +
77A GLU* 3.5 6.4 - - - +
78A ILE* 1.3 86.5 - - - +
80A ARG* 1.3 60.6 + - - -
81A PHE* 5.2 0.7 - - - -
98A ILE* 4.2 20.6 - - - -
100A VAL* 5.6 0.2 - - - -
187A THR* 6.0 2.9 - - - -
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Residues in contact with ARG 80 (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* 4.0 17.5 - - + -
63A ALA 3.1 14.8 - - - +
64A ASN* 3.5 2.0 - - + +
77A GLU* 3.1 37.3 + - - +
79A GLY* 1.3 74.3 - - - +
81A PHE* 1.3 68.0 + - - +
98A ILE* 4.1 4.1 - - - +
152A ASN* 3.9 3.2 - - - +
187A THR* 2.8 48.9 + - + +
188A ILE* 4.0 0.2 - - - +
189A SER* 3.0 24.8 + - - +
256A ALA* 3.6 4.9 - - - +
257A VAL* 2.9 39.7 + - + +
294A ALA* 2.8 35.7 + - - +
295A ILE* 3.4 11.1 - - - +
296A SER 3.4 1.6 - - - +
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Residues in contact with PHE 81 (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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47A ILE* 3.7 35.4 - - + -
49A ASN* 5.9 1.6 - - + -
62A TYR* 5.1 0.3 - - - -
63A ALA* 3.0 60.1 + - + +
64A ASN 4.5 2.2 - - - -
65A VAL* 4.7 9.9 - - + -
79A GLY 5.1 0.4 - - - -
80A ARG* 1.3 82.5 - - - +
82A ILE* 1.3 77.6 + - - +
83A THR* 4.1 10.8 - - + -
84A PRO* 6.0 0.7 - - + -
96A LEU* 3.6 25.1 - - + -
98A ILE* 4.8 0.9 - - + -
115A ILE* 4.7 4.9 - - + -
127A TYR* 3.8 29.6 - + - -
255A MET 3.4 15.5 - - - +
256A ALA* 3.7 9.4 - - + +
257A VAL* 4.0 3.4 - - - +
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Residues in contact with ILE 82 (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* 3.9 18.8 - - + +
61A ARG 3.4 8.5 - - - +
62A TYR* 4.2 23.3 - - + -
80A ARG* 5.9 0.2 - - - -
81A PHE* 1.3 88.3 - - - +
83A THR* 1.3 70.6 + - - +
84A PRO* 4.2 0.3 - - - +
96A LEU* 5.1 0.2 - - - +
189A SER* 5.0 4.5 - - - +
251A TRP* 3.5 47.8 - - + -
252A CYS 3.7 13.5 - - - +
253A PRO* 4.0 2.5 - - + -
254A GLY* 2.8 24.8 + - - -
255A MET 3.1 7.9 + - - +
257A VAL* 4.2 19.1 - - + -
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Residues in contact with THR 83 (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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49A ASN* 4.9 0.9 - - - +
59A TRP 3.0 10.2 + - - -
60A ASP* 3.2 17.8 - - - +
61A ARG* 2.7 45.7 + - - +
63A ALA* 4.7 0.7 - - + -
81A PHE* 4.1 14.8 - - + -
82A ILE* 1.3 76.2 - - - +
84A PRO* 1.3 73.9 - - + +
117A THR* 4.6 4.5 - - + -
125A ARG* 3.8 23.8 + - + +
127A TYR* 3.5 26.2 - - + +
254A GLY 3.3 3.5 + - - -
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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