Contacts of the strand formed by residues 79 - 87 (chain H) 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 PHE 79 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H HIS* 3.2 33.2 - + + -
7H THR* 3.9 22.4 - - + +
37H HIS* 3.9 16.2 - + - -
69H HIS 3.6 0.7 - - - +
70H GLN* 3.5 1.7 - - - +
71H TRP* 2.7 75.4 + + + +
73H ALA* 4.2 4.0 - - + -
77H THR* 3.5 39.3 - - + -
78H PRO* 1.3 72.3 - - - +
80H LEU* 1.3 73.6 + - - +
81H ARG* 3.9 6.1 - - + +
158H SO4 5.0 11.0 - - - -
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H PRO* 3.6 29.6 - - + -
5H HIS 2.7 12.8 + - - +
6H VAL* 3.4 18.0 - - + +
7H THR* 2.9 28.3 + - - +
68H MET* 3.9 24.0 - - + -
69H HIS 3.5 2.2 - - - -
70H GLN* 3.5 35.9 - - + +
79H PHE* 1.3 83.7 - - - +
81H ARG* 1.3 59.5 + - - +
82H PHE* 3.9 8.0 + - + -
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Residues in contact with ARG 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H THR* 3.2 19.3 - - - +
9H ALA* 3.4 29.9 - - + +
32H ASN* 3.3 18.0 + - - -
33H GLN* 2.9 22.8 + - - -
35H ALA* 4.0 0.6 - - - +
67H ARG 3.8 0.3 - - - +
68H MET* 3.0 4.2 - - - +
69H HIS* 2.6 55.1 + - + +
71H TRP* 6.1 0.2 - - - -
79H PHE* 5.0 6.3 - - + -
80H LEU* 1.3 69.9 - - - +
82H PHE* 1.3 61.3 + - - +
83H LEU* 3.7 6.1 + - + +
120H SER* 5.4 2.3 + - - -
122H LEU* 3.5 37.0 + - + +
123H VAL* 4.9 1.8 - - - +
126H SER* 2.9 25.1 + - - -
158H SO4 3.0 24.5 + - - +
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Residues in contact with PHE 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 3.8 20.0 - - + -
7H THR 2.8 21.2 + - - +
8H VAL* 3.4 3.6 - - - -
9H ALA 2.9 28.5 + - - +
44H LEU* 3.7 28.9 - - + -
65H PHE* 3.6 17.9 - + + -
67H ARG 3.7 1.6 - - - -
68H MET* 3.3 44.4 - - + -
80H LEU* 4.0 12.1 - - + -
81H ARG* 1.3 72.7 - - - +
83H LEU* 1.3 59.5 + - - +
84H PHE* 3.8 16.4 - - + -
141H ILE* 3.7 24.0 - - + -
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ALA* 4.0 20.6 - - + -
10H CYS 4.4 0.9 - - - +
11H VAL* 3.9 22.0 - - + +
33H GLN* 4.8 0.9 - - + -
65H PHE* 3.4 7.3 - - - -
66H ILE* 2.8 53.8 + - + -
67H ARG* 2.5 22.5 + - + +
69H HIS* 4.8 9.2 - - + +
81H ARG* 3.7 6.9 + - - +
82H PHE* 1.3 72.5 - - - +
84H PHE* 1.3 61.7 + - - +
126H SER* 3.4 54.3 - - - +
129H CYS* 4.4 4.0 - - + -
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Residues in contact with PHE 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H VAL* 4.3 8.3 - - + -
9H ALA 3.2 17.1 + - - +
10H CYS* 3.5 8.1 - - - -
11H VAL* 2.8 31.4 + - - +
44H LEU* 4.4 9.0 - - + -
45H VAL* 4.4 8.5 - - + -
48H ALA* 3.6 29.6 - - + -
62H PRO* 4.1 15.9 - - + -
64H HIS 3.3 16.4 - - - +
65H PHE* 3.6 26.7 - + + -
66H ILE* 3.2 9.3 - - - +
82H PHE* 3.8 20.6 - - + -
83H LEU* 1.3 72.7 - - - +
85H ALA* 1.3 56.8 + - - +
138H LEU* 3.7 26.0 - - + -
141H ILE* 3.9 21.1 - - + -
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Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H VAL 3.6 4.9 - - - +
63H GLN* 2.9 29.0 + - - +
64H HIS* 2.8 30.1 + - + +
66H ILE* 3.2 22.1 - - + +
84H PHE* 1.3 72.2 - - - +
86H ILE* 1.3 63.9 + - - +
87H GLU* 4.4 4.7 - - + +
130H TYR* 4.8 15.0 - - + -
135H ARG* 5.3 5.2 - - + +
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Residues in contact with ILE 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H CYS* 3.7 28.7 - - - -
11H VAL 2.9 13.2 + - - +
12H VAL* 3.3 27.6 - - + -
13H HIS* 2.9 28.8 + - - +
52H LEU* 4.3 8.5 - - + -
60H ALA* 4.3 19.5 - - + +
61H GLN 3.7 17.7 - - - +
62H PRO* 3.7 15.7 - - + -
63H GLN* 3.8 15.9 - - - +
84H PHE 5.3 0.2 - - - -
85H ALA* 1.3 80.3 - - - +
87H GLU* 1.3 70.8 + - - +
88H LEU* 4.2 8.5 - - + -
130H TYR* 6.3 0.2 - - - -
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Residues in contact with GLU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU* 4.0 20.6 - - - +
128B ARG* 3.4 30.9 + - - +
13H HIS* 2.7 34.8 - - - +
63H GLN* 3.0 29.6 + - - +
64H HIS* 6.2 0.4 - - - +
85H ALA* 5.2 4.7 - - + +
86H ILE* 1.3 74.8 - - - +
88H LEU* 1.3 66.9 + - - +
130H TYR* 2.8 32.4 + - - -
135H ARG* 4.9 6.2 + - - +
144L PHE* 5.4 5.2 - - + -
145L ASN* 3.7 12.4 - - - +
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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