Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 3SHD
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 HIS 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A PRO 3.7 0.2 - - - -
63A GLN* 1.3 105.1 + - + +
65A PHE* 1.3 61.6 + - - +
66A ILE 3.5 0.2 + - - -
84A PHE* 3.4 6.9 - - - -
85A ALA* 3.1 35.2 + - + +
135A ARG* 3.4 63.5 + - + -
136A TYR* 3.1 20.4 - - - +
137A PRO* 4.8 0.2 - - + -
138A LEU* 4.0 10.8 - - - -
139D GLU* 3.5 29.2 + - - -
67E ARG* 4.9 6.9 + - - -
125E GLU* 3.9 6.5 - - - -
129E CYS* 5.7 0.8 - - - -
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Residues in contact with PHE 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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64A HIS* 1.3 71.5 - - - +
66A ILE* 1.3 64.8 + - - +
67A ARG* 3.0 40.8 - - - -
68A MET* 3.6 11.9 - - + -
82A PHE* 3.6 19.7 - + + -
83A LEU 3.5 13.0 - - - -
84A PHE* 3.8 20.9 - + + -
135A ARG* 4.5 0.2 - - - -
136A TYR* 2.8 43.9 + + + +
137A PRO 4.0 12.6 - - - +
138A LEU* 4.1 5.2 - - - +
140A MET* 3.9 21.1 - - + -
141A ILE* 3.9 23.3 - - + -
65I PHE* 5.7 0.4 - + - -
140I MET* 4.2 21.1 - - + -
141I ILE* 5.3 2.7 - - + -
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Residues in contact with ILE 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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11A VAL* 3.8 20.9 - - + -
64A HIS 3.5 0.8 + - - -
65A PHE* 1.3 76.0 - - - +
67A ARG* 1.3 64.9 + - + +
83A LEU* 2.8 22.1 + - + +
84A PHE 3.6 22.2 - - - +
85A ALA* 3.7 23.8 - - + -
129A CYS* 3.8 30.3 - - + -
130A TYR* 4.3 14.4 - - + -
134A GLN* 3.4 29.5 - - + +
135A ARG* 4.4 3.1 - - + +
136A TYR* 3.3 22.7 - - - -
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Residues in contact with ARG 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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65A PHE* 3.0 22.1 - - - -
66A ILE* 1.3 92.6 - - + +
68A MET* 1.3 65.9 + - - +
69A HIS* 3.5 39.7 + - + -
83A LEU* 2.8 33.9 + - + +
125A GLU* 5.7 0.2 + - - -
129A CYS* 4.0 11.2 - - - -
134A GLN* 4.0 12.1 - - - +
139I GLU* 2.8 42.1 + - - +
140I MET* 3.6 18.2 - - - +
142I GLY* 2.7 40.0 + - - +
143I ASP 4.4 4.0 + - - -
64K HIS* 4.7 7.7 + - - -
135K ARG* 5.4 0.4 - - - +
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Residues in contact with MET 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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65A PHE* 3.9 10.8 - - + -
67A ARG* 1.3 98.4 + - - +
69A HIS* 1.3 63.7 + - - +
70A GLN* 3.8 22.0 - - + +
80A LEU* 3.9 12.3 - - + -
81A ARG 3.3 22.0 - - - +
82A PHE* 3.7 31.2 - - + -
44I LEU* 3.9 13.2 - - + -
82I PHE* 3.8 17.3 - - - -
140I MET 3.1 16.2 + - - +
141I ILE* 3.2 40.8 - - + +
142I GLY 3.6 0.9 - - - +
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Residues in contact with HIS 69 (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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67A ARG* 3.5 42.7 + - + -
68A MET* 1.3 78.7 - - - +
70A GLN* 1.3 59.9 + - - +
71A TRP* 3.9 1.1 + - - -
79A PHE 3.8 0.9 - - - +
80A LEU* 3.7 1.0 - - - -
81A ARG* 2.9 46.0 + - + +
83A LEU* 4.5 20.0 - - + +
122A LEU* 3.6 36.0 - - + +
125A GLU* 3.6 15.7 + - + +
126A SER* 5.0 4.3 - - - -
129A CYS* 3.6 22.3 - - - -
142I GLY 3.7 2.5 - - - -
144I PHE* 4.1 17.7 - + + -
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Residues in contact with GLN 70 (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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68A MET* 3.8 8.2 - - + +
69A HIS* 1.3 72.4 - - - +
71A TRP* 1.3 59.3 + - - +
72A ILE* 5.8 0.7 - - + -
79A PHE 3.3 6.7 - - - +
80A LEU* 3.8 20.8 - - + +
38I LEU* 4.0 20.6 - - - +
42I GLU 2.6 27.6 + - - -
43I THR* 3.2 12.7 - - - +
44I LEU* 3.1 28.5 + - - +
141I ILE 4.6 0.3 - - - +
142I GLY 3.1 8.6 + - - +
143I ASP* 3.1 13.3 + - - +
144I PHE 2.9 24.7 + - - -
146I TRP* 3.7 20.9 - - + -
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Residues in contact with TRP 71 (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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69A HIS 3.9 1.7 + - - -
70A GLN* 1.3 77.4 - - - +
72A ILE* 1.3 65.5 + - - +
73A ALA* 3.5 40.6 - - + -
74A PRO* 3.7 13.0 - - + -
79A PHE* 3.0 62.1 + + + +
81A ARG* 5.7 0.6 - - - +
120A SER* 4.1 17.0 - - - -
121A PRO* 3.7 35.7 - - + -
122A LEU* 3.3 33.4 - - + +
144I PHE* 3.5 28.3 - + + +
145I ASN* 5.1 7.9 - - + -
146I TRP* 4.6 2.9 - - - -
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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