Contacts of the strand formed by residues 64 - 71 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139H GLU* 3.4 30.1 + - - +
63L GLN* 1.3 107.8 + - + +
65L PHE* 1.3 60.7 + - - +
84L PHE* 3.2 9.0 - - - +
85L ALA* 2.8 36.6 + - + +
135L ARG* 3.3 66.1 + - + -
136L TYR 3.5 14.8 - - - +
138L LEU* 3.5 7.8 - - - +
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Residues in contact with PHE 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 5.8 0.4 - + - -
140B MET* 3.9 20.4 - - + -
141B ILE* 5.4 2.7 - - + -
64L HIS* 1.3 71.9 - - - +
66L ILE* 1.3 62.4 + - - +
67L ARG* 3.4 41.5 - - - -
68L MET* 3.7 6.5 - - + -
82L PHE* 3.6 34.3 - + + -
83L LEU 3.7 8.1 - - - -
84L PHE* 4.2 11.4 - + + -
135L ARG* 3.7 0.5 - - - -
136L TYR* 2.9 36.8 + - + +
137L PRO 3.9 17.7 - - - +
138L LEU* 3.6 8.9 - - + +
140L MET* 4.1 17.7 - - + -
141L ILE* 3.9 29.8 - - + -
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Residues in contact with ILE 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B MET* 4.1 1.9 - - - +
11L VAL* 3.9 19.7 - - + -
64L HIS 3.7 0.2 + - - -
65L PHE* 1.3 78.4 - - - +
67L ARG* 1.3 68.0 + - + +
83L LEU* 2.8 23.1 + - + +
84L PHE 3.7 21.8 - - - +
85L ALA* 3.7 24.2 - - + -
129L CYS* 3.9 28.9 - - + -
130L TYR* 4.0 18.8 - - + +
134L GLN* 3.6 31.3 + - - +
135L ARG* 5.4 2.9 - - + -
136L TYR* 3.8 13.3 - - - -
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Residues in contact with ARG 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLU* 2.9 25.9 + - - +
140B MET* 3.7 18.4 - - + +
142B GLY* 2.9 29.9 + - - +
143B ASP 4.5 4.0 + - - -
64G HIS* 5.0 13.3 + - - -
65L PHE* 3.4 20.3 - - - -
66L ILE* 1.3 86.0 - - + +
68L MET* 1.3 82.4 + - - +
69L HIS* 3.0 41.4 + - + -
83L LEU* 2.9 32.7 + - + +
125L GLU* 5.3 1.6 + - - -
129L CYS* 3.9 13.2 - - - -
134L GLN* 3.7 18.6 - - - +
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Residues in contact with MET 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.9 13.5 - - + -
82B PHE* 3.9 11.9 - - - -
140B MET 3.3 6.1 + - - -
141B ILE* 2.9 47.4 - - + +
142B GLY 3.5 3.1 - - - +
65L PHE* 3.9 13.7 - - + -
67L ARG* 1.3 97.5 + - - +
69L HIS* 1.3 65.9 + - - +
70L GLN* 3.8 24.9 - - + +
80L LEU* 3.7 22.9 - - + -
81L ARG 3.2 21.1 - - - +
82L PHE* 3.7 26.9 - - + -
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Residues in contact with HIS 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLY 3.5 1.6 - - - -
143B ASP 5.5 0.2 - - - -
144B PHE* 4.1 18.8 - + + -
67L ARG* 3.0 48.8 + - + -
68L MET* 1.3 78.8 - - - +
70L GLN* 1.3 60.0 + - - +
71L TRP* 3.9 1.5 + - - -
79L PHE 3.7 1.6 - - - +
80L LEU* 3.5 1.0 - - - -
81L ARG* 2.7 51.4 + - + +
83L LEU* 4.1 20.2 - - + +
122L LEU* 3.4 41.0 - - + +
125L GLU* 3.7 18.3 + - + -
126L SER* 5.2 1.8 - - - -
129L CYS* 3.9 11.9 - - - -
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Residues in contact with GLN 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 4.4 10.9 - - - +
42B GLU 2.6 27.5 + - - -
43B THR* 3.4 8.9 - - - +
44B LEU* 3.2 26.4 + - - +
141B ILE 4.6 1.1 - - - +
142B GLY 3.0 13.4 + - - +
143B ASP* 3.2 11.1 + - - +
144B PHE 2.9 25.4 + - - -
146B TRP* 3.7 23.9 - - + -
2L PHE* 5.8 2.6 - - - -
68L MET* 3.8 8.1 - - + +
69L HIS* 1.3 71.1 - - - +
71L TRP* 1.3 61.6 + - - +
79L PHE 3.2 6.1 - - - +
80L LEU* 3.5 27.6 - - + +
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Residues in contact with TRP 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE* 3.4 34.8 - + + +
145B ASN* 5.5 6.5 - - + -
146B TRP* 4.1 5.8 - - - -
69L HIS 3.9 3.1 - - - -
70L GLN* 1.3 74.8 - - - +
72L ILE* 1.3 80.1 + - - +
73L ALA* 3.8 16.6 - - + -
74L PRO* 3.9 23.3 - - + -
78L PRO* 3.6 0.9 - - - +
79L PHE* 2.7 67.7 + + + +
81L ARG* 5.3 3.6 - - + +
120L SER* 4.0 27.1 - - - -
121L PRO* 4.7 13.7 - - + -
122L LEU* 3.7 27.3 - - + +
158L SO4 4.9 8.6 + - - -
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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