Contacts of the strand formed by residues 72 - 79 (chain A) in PDB entry 3ID8
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A VAL* 1.3 77.5 - - - +
73A ASP* 1.3 66.5 + - - -
74A PHE* 3.7 5.7 - - - -
89A VAL 3.5 1.4 - - - +
90A LYS* 3.3 9.4 - - - -
91A VAL* 2.7 43.1 + - - +
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Residues in contact with ASP 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 VAL 4.3 0.6 + - - -
72A GLY* 1.3 74.5 - - - +
74A PHE* 1.3 66.2 + - - +
88A LEU* 3.9 24.1 - - + +
89A VAL 3.6 1.6 - - - -
90A LYS* 3.7 25.1 - - - +
103A THR* 5.6 0.2 + - - -
139A MET* 5.9 0.3 - - - +
142A LYS* 5.7 6.0 + - + +
144A LEU* 3.6 20.0 - - + +
145A PRO* 3.4 22.0 - - - +
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Residues in contact with PHE 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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70A GLU* 4.6 5.6 - - + -
71A VAL 4.4 10.5 - - - -
72A GLY 3.7 21.1 - - - -
73A ASP* 1.3 77.2 - - - +
75A LEU* 1.3 62.4 + - - +
76A SER 4.1 0.4 - - - -
88A LEU* 3.3 9.4 - - - +
89A VAL* 2.9 31.6 + - - +
91A VAL* 4.1 15.9 - - + -
144A LEU* 4.1 4.5 - - - -
145A PRO* 3.6 39.3 - - + +
147A GLY 6.0 0.4 - - - +
450A ALA* 3.7 24.7 - - + -
453A SER* 3.7 19.7 - - - -
454A ALA* 3.5 40.8 - - + -
457A CYS* 3.9 10.1 - - - -
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Residues in contact with LEU 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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74A PHE* 1.3 74.2 - - - +
76A SER* 1.3 60.7 + - - +
77A LEU* 4.3 7.4 - - + -
86A VAL* 3.8 13.9 - - + -
87A MET 3.4 11.7 - - - +
88A LEU* 4.4 2.0 - - + +
130A ILE* 4.8 9.6 - - + -
133A PHE* 3.5 33.2 - - + -
134A LEU* 4.2 18.8 - - + -
139A MET* 4.4 6.5 - - + -
144A LEU* 4.4 6.9 - - + +
145A PRO 3.0 10.4 + - - +
146A LEU* 3.1 27.9 - - + +
147A GLY 2.9 24.8 + - - -
197A MET* 4.0 22.7 - - + -
450A ALA* 6.2 0.2 - - - -
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Residues in contact with SER 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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74A PHE 4.1 0.6 - - - -
75A LEU* 1.3 73.2 - - - +
77A LEU* 1.3 67.6 + - - +
85A ARG 3.8 0.2 - - - +
86A VAL* 3.4 5.9 - - - +
87A MET* 2.7 45.4 + - - -
89A VAL* 3.8 5.4 - - - +
147A GLY* 3.4 5.3 - - - -
446A GLY* 2.6 42.7 + - - -
449A ALA* 3.5 5.6 - - - +
450A ALA* 3.5 13.0 + - - +
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Residues in contact with LEU 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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75A LEU* 4.3 0.7 - - + -
76A SER* 1.3 83.8 - - - +
78A ASP* 1.3 61.8 - - - +
84A PHE* 3.9 15.3 - - + -
85A ARG 3.4 3.8 - - - -
86A VAL* 4.1 11.2 - - + -
126A ILE* 5.0 0.4 - - + -
130A ILE* 3.8 37.0 - - + -
146A LEU* 3.7 29.8 - - + -
147A GLY 2.9 10.3 + - - +
148A PHE* 3.7 19.7 - - + -
149A THR* 2.9 30.5 + - - -
185A LEU* 3.8 31.2 - - + -
445A SER* 4.7 0.3 + - - -
446A GLY* 6.4 0.2 - - - -
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Residues in contact with ASP 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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77A LEU* 1.3 76.6 - - - +
79A LEU* 1.3 68.6 + - - +
80A GLY* 4.1 3.1 + - - -
81A GLY 5.3 0.9 + - - -
83A ASN 4.0 3.3 - - - +
84A PHE* 3.3 9.7 - - - -
85A ARG* 2.8 55.6 + - + +
149A THR* 3.4 13.6 - - - +
151A SER* 5.0 2.1 + - - -
205A ASP* 5.1 2.9 - - - +
445A SER* 2.5 35.8 + - - +
446A GLY* 6.2 0.7 - - - -
600A ANP 5.7 1.0 + - - -
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Residues in contact with LEU 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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78A ASP* 1.3 78.3 + - - +
80A GLY* 1.3 58.7 + - - +
83A ASN 4.9 0.2 - - - -
84A PHE* 4.1 11.2 - - + -
110A ILE* 3.8 20.4 - - + -
122A LEU* 4.3 17.9 - - + -
123A PHE* 4.7 1.8 - - + -
126A ILE* 3.7 26.9 - - + -
148A PHE* 3.9 17.2 - - + -
149A THR 2.9 9.6 + - - +
150A PHE* 3.7 28.2 - - + -
151A SER* 3.0 25.8 + - - -
152A PHE* 3.8 7.1 - - + -
171A PHE* 3.7 27.6 - - + -
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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