Contacts of the strand formed by residues 64 - 71 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63G GLN* 1.3 112.9 + - + +
65G PHE* 1.3 60.2 + - - +
84G PHE* 3.0 26.7 - - - +
85G ALA* 3.1 20.7 + - + +
135G ARG* 2.9 62.9 + - + -
136G TYR 3.7 16.6 - - - +
137G PRO* 5.1 3.6 - - + -
138G LEU* 3.5 10.9 - - - +
67L ARG* 5.0 11.8 + - - -
125L GLU* 4.3 5.3 + - - -
129L CYS* 5.5 1.4 - - - -
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Residues in contact with PHE 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C MET* 3.3 36.6 - - + -
141C ILE* 4.3 2.2 - - + -
64G HIS* 1.3 73.4 - - - +
66G ILE* 1.3 63.0 + - - +
67G ARG* 3.5 35.4 - - - -
68G MET* 3.6 7.2 - - + -
82G PHE* 3.6 24.9 - + + -
83G LEU 3.8 6.1 - - - -
84G PHE* 3.7 23.1 - + + -
135G ARG* 3.5 1.7 - - - -
136G TYR* 2.6 47.3 + - + +
137G PRO 3.9 10.1 - - - +
138G LEU* 3.9 4.9 - - - +
140G MET* 4.2 12.3 - - + -
141G ILE* 3.5 23.1 - - + -
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Residues in contact with ILE 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 4.1 11.2 - - + -
65G PHE* 1.3 74.4 - - - +
67G ARG* 1.3 64.9 + - + +
83G LEU* 2.7 37.5 + - + +
84G PHE 3.6 20.9 - - - +
85G ALA* 3.6 23.3 - - + +
129G CYS* 4.1 25.1 - - + +
130G TYR* 4.4 12.6 - - + -
134G GLN* 3.2 45.9 - - + +
135G ARG* 5.4 1.3 - - + -
136G TYR* 3.6 13.6 - - - -
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Residues in contact with ARG 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLU* 3.1 42.1 + - - +
140C MET* 3.2 14.6 - - + +
142C GLY* 2.5 44.3 + - - +
143C ASP 4.1 4.8 + - - -
144C PHE* 5.8 1.0 - - - -
65G PHE* 3.5 15.7 - - - -
66G ILE* 1.3 86.2 - - + +
68G MET* 1.3 70.9 + - - +
69G HIS* 3.3 40.2 + - + -
81G ARG 4.0 0.2 - - - +
83G LEU* 2.9 32.4 + - + +
125G GLU* 5.6 1.4 + - - -
129G CYS* 4.0 16.8 - - - -
134G GLN* 4.1 14.0 - - - +
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Residues in contact with MET 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 4.2 6.3 - - + -
82C PHE* 3.9 14.1 - - - -
140C MET 3.0 4.9 + - - -
141C ILE* 3.4 48.5 - - + +
142C GLY 3.6 0.7 - - - +
65G PHE* 3.6 1.5 - - + -
67G ARG* 1.3 97.6 + - - +
69G HIS* 1.3 80.9 + - - +
70G GLN* 3.7 8.7 - - + +
80G LEU* 3.7 25.6 - - + -
81G ARG 3.2 22.2 - - - +
82G PHE* 3.7 40.6 - - + -
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Residues in contact with HIS 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C GLY 3.7 0.9 - - - -
144C PHE* 3.9 27.1 - + + -
67G ARG* 3.3 45.1 + - + +
68G MET* 1.3 75.4 - - - +
70G GLN* 1.3 61.1 + - - +
71G TRP 3.8 1.1 + - - -
79G PHE* 3.7 1.2 - - - +
80G LEU* 3.5 3.6 - - - -
81G ARG* 2.8 44.9 + - + +
83G LEU* 5.0 9.3 - - + +
122G LEU* 3.6 31.9 - - + +
125G GLU* 3.7 21.6 + - + +
126G SER* 5.0 6.4 + - - -
129G CYS* 3.6 25.9 - - + -
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Residues in contact with GLN 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.3 11.5 - - - +
42C GLU 2.7 26.4 + - - -
43C THR* 3.3 9.4 + - - +
44C LEU* 3.2 28.5 + - - +
141C ILE 4.8 1.6 - - - +
142C GLY 3.0 11.3 + - - +
143C ASP* 3.1 15.8 + - - +
144C PHE 2.9 22.9 + - - -
146C TRP* 3.7 21.9 - - + -
2G PHE* 6.2 1.2 - - - -
68G MET* 3.7 14.7 - - + +
69G HIS* 1.3 71.7 - - - +
71G TRP* 1.3 62.0 + - - +
79G PHE 3.5 4.0 - - - +
80G LEU* 3.7 20.4 - - + +
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Residues in contact with TRP 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.8 35.7 - + + +
145C ASN* 4.7 7.6 - - + -
146C TRP* 4.2 4.4 - - - -
69G HIS 3.8 1.4 + - - -
70G GLN* 1.3 76.7 - - - +
72G ILE* 1.3 66.4 + - - +
73G ALA* 3.2 40.8 - - + +
74G PRO* 4.3 9.0 - - + -
78G PRO* 3.7 0.3 - - - +
79G PHE* 2.7 63.0 + - + +
120G SER* 4.1 15.5 - - - -
121G PRO* 3.2 48.2 - - + -
122G LEU* 3.9 25.4 - - + +
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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