Contacts of the strand formed by residues 72 - 78 (chain A) in PDB entry 1A16
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLN* 3.2 32.6 + - - +
16A VAL* 3.7 32.8 - - + +
65A ILE 3.0 15.7 - - - +
66A LYS* 4.0 3.5 - - + +
67A SER* 4.4 1.1 - - - +
68A ASP 5.4 1.0 + - - -
69A ASP 5.6 1.4 + - - -
70A THR 3.8 13.1 + - - -
71A HIS* 1.3 77.6 - - - +
73A HIS* 1.3 68.0 + - - +
105A ASP* 4.5 1.0 - - - +
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Residues in contact with HIS 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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63A VAL 3.9 0.2 - - - +
64A LEU* 3.9 2.3 - - - +
65A ILE* 2.9 74.1 + - + +
67A SER* 4.5 8.7 + - - -
72A ASN* 1.3 79.3 + - - +
74A SER* 1.3 64.1 + - - +
75A VAL* 3.9 18.8 - - + +
105A ASP* 3.2 20.2 - - + +
106A ARG* 4.9 13.4 + - - -
120A LEU* 5.4 2.4 - - - +
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Residues in contact with SER 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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12A ARG* 5.2 3.7 + - - -
62A LEU* 4.5 1.8 - - - -
63A VAL 3.3 4.0 - - - -
64A LEU* 3.7 24.5 - - - -
73A HIS* 1.3 74.4 - - - +
75A VAL* 1.3 67.3 + - - +
103A GLY 4.3 2.6 + - - -
104A VAL* 3.2 20.7 - - - +
105A ASP* 3.0 32.4 + - - +
106A ARG 3.1 21.7 + - - -
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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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61A VAL 3.7 1.4 - - - +
62A LEU* 3.9 3.5 - - - +
63A VAL* 2.8 43.2 + - + +
65A ILE* 4.2 11.9 - - + -
73A HIS* 3.9 23.6 - - + +
74A SER* 1.3 79.4 - - - +
76A LEU* 1.3 62.6 + - - +
77A PHE* 4.3 14.8 - - + -
104A VAL* 5.3 0.4 - - - -
106A ARG* 3.5 22.9 - - + +
108A LEU* 4.1 31.9 - - + -
120A LEU* 4.3 10.5 - - + -
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Residues in contact with LEU 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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49A PHE* 4.4 18.2 - - + -
53A THR* 5.1 4.7 - - + -
55A PHE* 4.4 5.6 - - + -
60A ALA* 4.6 2.5 - - + -
61A VAL 3.5 17.5 - - - +
62A LEU* 4.4 12.1 - - + -
75A VAL* 1.3 74.3 - - - +
77A PHE* 1.3 65.4 + - - +
78A ASN* 3.7 26.7 - - + +
98A ALA* 4.0 9.4 - - + -
102A LEU* 3.7 29.2 - - + -
104A VAL* 4.1 15.0 - - + +
106A ARG 2.9 14.0 + - - +
107A ALA* 3.0 6.8 - - - +
108A LEU* 2.6 33.1 + - - +
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Residues in contact with PHE 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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59A GLU 4.5 0.7 - - - -
60A ALA* 2.9 7.9 - - - +
61A VAL* 2.9 41.7 + - + +
63A VAL* 3.9 21.5 - - + -
75A VAL* 4.3 4.5 - - + -
76A LEU* 1.3 75.2 - - - +
78A ASN* 1.3 63.2 + - - +
108A LEU* 3.0 35.2 - - + +
109A ALA 3.6 17.9 - - - -
110A PHE* 4.1 13.7 - - + -
113A ILE* 3.8 35.2 - - + -
116A GLN* 3.7 27.4 - - + -
117A LEU* 4.2 8.7 - - + -
120A LEU* 3.9 22.7 - - + -
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Residues in contact with ASN 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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55A PHE* 3.9 26.4 - - + -
57A GLU* 5.1 1.3 + - + +
59A GLU 3.6 8.5 - - - -
60A ALA* 4.2 1.3 - - + -
76A LEU* 3.7 26.7 - - + +
77A PHE* 1.3 77.4 - - - +
79A ARG* 1.3 61.2 + - - +
80A VAL 3.3 0.2 + - - -
93A LEU* 4.1 2.8 - - - +
94A GLY 3.0 35.1 + - - +
95A GLN* 2.6 43.7 - - - +
98A ALA* 4.1 1.6 - - - +
107A ALA* 4.0 5.7 - - - +
108A LEU 3.0 6.1 + - - +
109A ALA* 3.4 0.2 - - - -
110A PHE* 3.0 18.0 + - - +
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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