Contacts of the strand formed by residues 64 - 72 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E PRO 3.7 0.2 - - - -
63E GLN* 1.3 95.3 + - + +
65E PHE* 1.3 61.8 + - - +
84E PHE* 3.2 11.3 - - - +
85E ALA* 2.9 29.1 + - + +
135E ARG* 3.5 44.7 - - + -
136E TYR 3.8 11.4 - - - +
137E PRO* 5.4 2.2 - - + -
138E LEU* 3.5 9.0 - - - +
63F GLN* 5.1 1.3 - - - -
64F HIS* 3.6 31.1 - + - -
85F ALA* 5.9 1.1 - - + +
87F GLU* 3.8 28.6 + - + +
130F TYR* 5.5 0.4 - - - -
135F ARG* 3.8 22.8 + - + -
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Residues in contact with PHE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D MET* 3.2 33.4 - - + -
141D ILE* 5.0 1.1 - - + -
64E HIS* 1.3 72.7 - - - +
66E ILE* 1.3 64.1 + - - +
67E ARG 3.3 32.1 - - - -
68E MET* 3.5 11.2 - - + -
82E PHE* 4.2 14.1 - + + -
83E LEU 3.4 13.2 - - - -
84E PHE* 3.9 17.3 - + + -
135E ARG* 3.8 2.4 - - - -
136E TYR* 2.8 49.2 + - + +
137E PRO 3.8 11.9 - - - +
138E LEU* 3.7 8.6 - - - +
140E MET* 3.3 23.3 - - + -
141E ILE* 4.0 23.1 - - + -
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Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D MET* 3.6 10.6 - - - +
11E VAL* 4.3 11.2 - - + -
65E PHE* 1.3 76.2 - - - +
67E ARG* 1.3 68.2 + - + +
83E LEU* 2.7 34.6 + - + +
84E PHE 3.6 27.1 - - - +
85E ALA* 3.7 20.2 - - + +
129E CYS* 3.7 35.0 - - + +
130E TYR* 4.6 11.4 - - + -
134E GLN 4.6 9.5 - - - +
135E ARG* 4.7 11.9 - - - +
136E TYR* 3.8 12.0 - - - -
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Residues in contact with ARG 67 (chain E).
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* 4.9 7.4 + - - -
139D GLU* 3.3 38.7 + - + +
140D MET* 3.6 27.4 - - + +
142D GLY* 3.0 37.2 + - - +
143D ASP 4.4 5.5 + - - -
144D PHE* 4.9 0.8 - - - +
65E PHE* 3.3 10.0 - - - -
66E ILE* 1.3 89.7 - - + +
68E MET* 1.3 75.9 + - - +
69E HIS* 3.2 39.9 + - + -
83E LEU* 2.8 29.4 + - + +
125E GLU* 5.7 1.2 + - - -
129E CYS* 4.1 11.1 - - - -
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Residues in contact with MET 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.3 3.6 - - + -
82D PHE* 4.0 24.0 - - - -
140D MET 2.8 16.2 + - - +
141D ILE* 4.0 23.1 - - + +
142D GLY 3.7 3.3 + - - -
65E PHE* 3.5 2.8 - - + -
67E ARG* 1.3 96.9 + - - +
69E HIS* 1.3 67.1 + - - +
70E GLN* 3.3 37.9 - - + +
80E LEU* 3.5 32.3 - - + -
81E ARG 3.3 22.4 - - - +
82E PHE* 3.8 25.8 - - + +
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Residues in contact with HIS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLY 3.4 4.9 - - - -
144D PHE* 3.9 18.2 - + + -
67E ARG* 3.2 49.1 + - + -
68E MET* 1.3 77.6 - - - +
70E GLN* 1.3 60.3 + - - +
71E TRP* 3.9 1.6 + - - +
79E PHE 3.8 1.2 - - - +
80E LEU* 3.7 0.7 - - - -
81E ARG* 2.9 42.4 + - + +
83E LEU* 4.5 15.6 - - + +
122E LEU* 3.4 39.9 - - + +
125E GLU* 4.0 9.9 + - + +
126E SER* 5.2 3.4 - - - -
129E CYS* 3.8 24.8 - - - -
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Residues in contact with GLN 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 4.5 7.3 - - - +
42D GLU 2.7 30.5 + - - -
43D THR* 3.4 15.6 + - - +
44D LEU* 3.0 29.7 + - - +
141D ILE 4.5 2.1 - - - +
142D GLY 2.6 15.9 + - - +
143D ASP* 3.1 10.7 + - - +
144D PHE 2.9 25.6 + - - +
146D TRP* 3.8 17.9 - - + -
68E MET* 3.3 14.2 - - + +
69E HIS* 1.3 70.3 - - - +
71E TRP* 1.3 64.5 + - - +
79E PHE 3.5 5.6 - - - +
80E LEU* 3.9 19.4 - - + +
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Residues in contact with TRP 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 3.2 42.6 - + + +
145D ASN* 4.4 11.4 + - + +
146D TRP* 4.8 2.9 - - - -
69E HIS 3.9 2.7 + - - +
70E GLN* 1.3 77.7 - - - +
72E ILE* 1.3 76.6 + - - +
73E ALA* 3.5 36.3 - - + -
74E PRO* 3.8 12.8 - - + -
78E PRO* 3.8 0.3 - - - +
79E PHE* 3.0 64.8 + + + +
81E ARG* 6.1 0.2 - - + -
120E SER* 4.0 28.3 - - - -
121E PRO* 4.9 7.7 - - + +
122E LEU* 4.2 28.9 - - + -
158E SO4 5.8 3.8 - - - -
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Residues in contact with ILE 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASP* 4.4 10.3 - - - +
144D PHE 5.1 0.2 + - - -
145D ASN 5.5 1.8 + - - +
146D TRP* 3.8 29.2 - - + -
147D PRO* 4.3 19.1 - - + +
148D PHE* 3.6 31.2 - - + -
71E TRP* 1.3 96.1 + - - +
73E ALA* 1.3 75.3 + - - +
76E LYS* 3.6 37.2 - - - +
77E THR 3.6 3.1 - - - +
78E PRO* 4.2 14.6 - - + -
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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