Contacts of the strand formed by residues 75 - 83 (chain A) in PDB entry 1C04
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 GLY 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE 3.7 1.0 + - - -
74A PRO* 1.3 74.3 - - - +
76A ARG* 1.3 59.0 + - - +
93A ILE* 3.9 9.0 - - - -
94A ASN 3.1 11.7 - - - -
95A TYR* 3.5 15.4 - - - -
96A ALA 4.6 0.2 - - - -
114A GLU* 3.3 9.0 - - - +
115A ILE 2.9 33.7 + - - -
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Residues in contact with ARG 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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75A GLY* 1.3 73.8 - - - +
77A VAL* 1.3 69.8 + - - +
78A ALA* 2.8 25.2 + - - +
93A ILE* 3.4 5.6 - - - +
94A ASN* 2.8 38.5 + - + +
111A VAL* 5.6 1.4 - - - +
112A GLY* 3.5 44.4 + - - +
113A MSE 3.8 2.9 - - - +
114A GLU* 5.1 6.3 - - + +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 1.3 74.9 + - - +
78A ALA* 1.3 61.2 + - - +
79A THR 3.9 6.7 - - - +
80A ILE* 3.7 31.0 - - + -
91A ALA* 4.1 5.8 - - + -
93A ILE* 3.5 14.4 - - + -
109A LEU* 3.7 16.4 - - + -
110A LYS 3.5 21.3 - - - +
111A VAL* 3.7 4.3 - - - +
112A GLY* 3.0 20.5 + - - +
113A MSE 2.9 23.4 + - - +
115A ILE* 3.3 24.2 - - + +
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Residues in contact with ALA 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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76A ARG* 2.8 17.7 + - - +
77A VAL* 1.3 73.0 - - - +
79A THR* 1.3 69.4 + - + +
92A LEU* 2.5 40.0 + - + +
94A ASN* 3.0 29.6 - - - +
111A VAL* 3.3 12.0 - - - +
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Residues in contact with THR 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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77A VAL* 3.5 0.7 - - - +
78A ALA* 1.3 89.8 - - + +
80A ILE* 1.3 68.8 + - - +
81A GLU* 3.0 21.5 + - - -
91A ALA* 3.0 6.8 - - - +
92A LEU* 2.9 40.8 + - + +
102A TYR* 5.0 0.3 + - - -
111A VAL* 3.5 9.2 - - + -
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Residues in contact with ILE 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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77A VAL* 3.7 17.0 - - + -
79A THR* 1.3 83.4 - - - +
81A GLU* 1.3 61.8 + - - +
89A ASN* 4.2 17.7 - - + +
90A ILE 3.3 4.9 - - - +
91A ALA* 3.8 7.2 - - + -
105A ALA* 3.9 19.3 - - + -
109A LEU* 3.0 42.2 - - + +
110A LYS* 3.7 11.9 - - - -
111A VAL* 3.9 7.7 - - + +
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Residues in contact with GLU 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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60A GLN* 5.9 0.3 + - - -
62A ARG* 3.5 27.0 + - - +
79A THR* 3.0 27.2 + - - -
80A ILE* 1.3 74.5 - - - +
82A TYR* 1.3 60.4 + - - +
89A ASN* 3.3 6.8 - - - -
90A ILE* 2.6 49.9 + - + +
102A TYR* 3.1 30.3 + - - -
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Residues in contact with TYR 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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62A ARG* 2.6 30.3 + - - -
81A GLU* 1.3 74.7 - - - +
83A ASP* 1.3 63.4 + - - +
84A PRO* 3.1 41.1 + - + +
87A SER* 3.0 44.2 + - - -
88A ALA* 3.8 4.3 - - - -
89A ASN* 3.3 19.2 + - - +
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Residues in contact with ASP 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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61A TYR* 4.5 1.1 - - - -
62A ARG* 3.5 20.1 + - - +
64A ILE* 4.8 0.2 - - - +
82A TYR* 1.3 77.3 - - - +
84A PRO* 1.3 52.7 - - - +
85A ASN* 2.6 37.8 + - - +
86A ARG* 2.8 48.4 + - + -
87A SER* 2.7 31.5 + - - -
88A ALA 2.8 18.3 + - - +
90A ILE* 3.9 24.9 - - + +
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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