Contacts of the strand formed by residues 64 - 71 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67F ARG* 4.0 8.0 + - - -
125F GLU* 4.6 4.7 - - - -
134F GLN* 6.1 0.4 - - - -
63I GLN* 1.3 105.8 + - + +
65I PHE* 1.3 61.1 + - - +
84I PHE* 3.2 9.0 - - - +
85I ALA* 3.0 36.8 + - + +
135I ARG* 3.5 63.1 + - + -
136I TYR* 3.3 15.3 - - - +
137I PRO* 4.7 0.4 - - + -
138I LEU* 3.5 8.3 - - - -
139K GLU* 2.9 38.7 + - + +
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Residues in contact with PHE 65 (chain I).
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* 5.7 0.4 - + - -
140A MET* 3.3 34.3 - - + -
141A ILE* 5.3 3.6 - - + -
64I HIS* 1.3 73.7 - - - +
66I ILE* 1.3 60.7 + - - +
67I ARG 3.3 34.5 - - - -
68I MET* 3.5 12.3 - - + -
82I PHE* 3.8 22.0 - + + -
83I LEU 4.0 4.3 - - - -
84I PHE* 4.1 13.0 - + + -
135I ARG 3.6 0.3 - - - -
136I TYR* 2.7 45.9 + - - +
137I PRO 3.9 10.8 - - - +
138I LEU* 3.6 10.5 - - + +
140I MET* 3.8 19.3 - - + -
141I ILE* 3.9 29.4 - - + -
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Residues in contact with ILE 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 3.9 10.2 - - - +
11I VAL* 4.3 10.5 - - + -
64I HIS 3.9 0.2 + - - -
65I PHE* 1.3 79.1 - - - +
67I ARG* 1.3 80.2 + - + +
83I LEU* 2.8 34.1 + - + +
84I PHE 3.5 21.8 - - - +
85I ALA* 3.6 23.3 - - + -
129I CYS* 3.9 21.1 - - + -
130I TYR* 4.3 17.3 - - + -
134I GLN* 3.7 24.8 + - - +
135I ARG* 4.7 6.5 - - + +
136I TYR* 3.9 5.2 - - - -
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Residues in contact with ARG 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU* 3.0 32.6 + - - +
140A MET* 3.7 15.0 - - + +
142A GLY* 2.9 32.7 + - - -
143A ASP 5.0 2.2 + - - -
64D HIS* 5.0 13.9 + - - -
65I PHE* 3.3 16.0 - - - -
66I ILE* 1.3 94.5 - - + +
68I MET* 1.3 70.6 + - - +
69I HIS* 3.1 41.6 + - + -
83I LEU* 2.6 38.2 + - + +
129I CYS* 3.9 13.8 - - - -
134I GLN* 3.7 12.8 - - - +
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Residues in contact with MET 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.0 2.5 - - + -
82A PHE* 3.7 32.8 - - - -
140A MET 3.0 16.7 + - - +
141A ILE* 3.1 40.3 - - + +
142A GLY 3.6 3.5 - - - +
65I PHE* 3.5 2.2 - - + -
67I ARG* 1.3 95.3 + - - +
69I HIS* 1.3 66.3 + - - +
70I GLN* 3.4 34.5 - - + +
80I LEU* 3.8 18.2 - - + -
81I ARG 3.0 13.7 - - - +
82I PHE* 3.5 29.4 - - + -
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Residues in contact with HIS 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 3.9 0.7 - - - -
144A PHE* 4.1 17.5 - + + -
67I ARG* 3.1 49.8 + - + +
68I MET* 1.3 76.9 - - - +
70I GLN* 1.3 60.3 + - - +
71I TRP* 3.8 3.5 + - - -
79I PHE 4.0 0.2 - - - +
80I LEU* 3.6 1.9 + - - -
81I ARG* 2.5 48.9 + - + +
83I LEU* 4.2 20.5 - - + +
122I LEU* 3.5 42.7 - - + +
125I GLU* 4.5 11.4 - - + +
126I SER* 5.2 2.0 - - - -
129I CYS* 4.2 16.7 - - - -
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Residues in contact with GLN 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.8 19.0 - - - +
42A GLU 2.7 26.2 + - - -
43A THR* 3.0 30.9 + - - +
44A LEU* 3.3 10.2 + - + +
141A ILE 4.3 2.4 - - - +
142A GLY 3.3 12.4 + - - +
143A ASP* 3.2 10.8 + - - +
144A PHE 2.9 25.7 + - - +
146A TRP* 4.0 17.4 - - + -
2I PHE* 5.9 1.6 - - - -
4I PRO* 6.4 0.2 - - - +
68I MET* 3.4 16.5 - - + +
69I HIS* 1.3 72.0 - - - +
71I TRP* 1.3 62.1 + - - +
79I PHE 3.5 11.9 - - - +
80I LEU* 3.8 9.0 - - + +
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Residues in contact with TRP 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.4 32.5 - + + +
145A ASN* 5.0 4.3 - - + +
146A TRP* 4.3 6.2 - - - -
69I HIS 4.3 6.5 - - - -
70I GLN* 1.3 75.5 - - - +
72I ILE* 1.3 64.6 + - - +
73I ALA* 3.3 43.7 - - + -
74I PRO* 4.2 11.2 - - + -
78I PRO* 3.9 1.6 - - - +
79I PHE* 2.9 64.5 + + + +
81I ARG* 5.0 5.0 - - + +
119I ARG* 5.8 1.8 - - - -
120I SER* 4.0 29.6 - - - -
121I PRO* 4.8 10.5 - - + -
122I LEU* 3.4 31.8 - - + +
158I SO4 5.1 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