Contacts of the strand formed by residues 79 - 87 (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 PHE 79 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L PRO* 4.9 0.9 - - - -
5L HIS* 3.6 22.0 - + + -
7L THR* 3.3 39.7 - - + +
37L HIS* 4.1 13.2 - + - -
70L GLN* 3.2 6.4 - - - +
71L TRP* 2.7 66.4 + + + +
72L ILE 3.9 4.0 - - - -
73L ALA* 4.5 6.3 - - + -
75L ASP* 5.3 0.4 - - - -
77L THR* 3.4 35.0 - - + -
78L PRO* 1.3 76.8 - - - +
80L LEU* 1.3 66.0 + - - +
81L ARG* 3.9 1.6 - - + +
158L SO4 4.4 11.9 - - - -
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Residues in contact with LEU 80 (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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6B VAL* 3.8 27.6 - - + -
38B LEU* 4.8 4.0 - - + -
44B LEU* 5.1 4.0 - - + -
80B LEU* 5.3 1.6 - - + -
82B PHE* 4.7 9.4 - - + -
4L PRO* 3.8 28.5 - - + +
5L HIS 3.1 9.8 + - - +
6L VAL* 3.5 15.4 - - + +
7L THR* 3.1 22.7 + - - +
68L MET* 3.7 22.7 - - + -
69L HIS 3.5 3.4 - - - -
70L GLN* 3.5 42.0 - - + +
79L PHE* 1.3 73.5 - - - +
81L ARG* 1.3 59.5 + - - +
82L PHE* 3.8 3.7 + - + -
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Residues in contact with ARG 81 (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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7L THR* 3.3 23.8 - - - +
9L ALA* 3.4 26.5 - - + +
32L ASN* 4.1 11.5 + - - -
33L GLN* 2.8 27.3 + - - +
35L ALA* 4.7 0.8 - - - +
68L MET* 3.2 6.8 - - - +
69L HIS* 2.7 49.7 + - + +
71L TRP* 5.3 1.3 - - + +
79L PHE* 5.0 5.6 - - + -
80L LEU* 1.3 69.6 - - - +
82L PHE* 1.3 67.4 + - - +
83L LEU* 3.6 6.0 + - + +
120L SER* 5.4 1.8 - - - -
122L LEU* 3.3 44.3 + - + +
123L VAL* 5.4 0.2 - - - +
126L SER* 2.8 24.8 + - - -
158L SO4 3.2 23.4 + - - +
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Residues in contact with PHE 82 (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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68B MET* 3.9 9.9 - - - -
80B LEU* 4.2 7.9 - - + -
82B PHE* 3.8 17.5 - + - -
141B ILE* 5.5 0.4 - - + -
6L VAL* 3.9 28.0 - - + -
7L THR 2.9 9.1 + - - +
8L VAL* 3.4 5.2 - - + -
9L ALA* 2.9 26.7 + - - +
44L LEU* 3.6 32.1 - - + -
65L PHE* 3.6 20.2 - + + -
67L ARG 4.0 2.0 - - - -
68L MET* 3.7 32.1 - - + -
80L LEU* 4.0 7.4 - - + -
81L ARG* 1.3 72.1 - - - +
83L LEU* 1.3 59.1 + - - +
84L PHE* 3.9 20.8 - - + -
141L ILE* 3.8 15.9 - - + -
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Residues in contact with LEU 83 (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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9L ALA* 3.5 23.6 - - + +
10L CYS 4.8 0.2 - - - -
11L VAL* 3.7 25.1 - - + +
33L GLN* 5.3 0.9 - - + +
65L PHE* 3.7 3.2 - - - -
66L ILE* 2.8 52.5 + - + +
67L ARG* 2.9 23.2 + - + +
69L HIS* 4.1 21.3 - - + +
81L ARG* 3.6 7.6 + - + +
82L PHE* 1.3 72.4 - - - +
84L PHE* 1.3 55.2 + - - +
126L SER* 3.6 40.4 - - - +
129L CYS* 4.2 4.0 - - + -
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Residues in contact with PHE 84 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8L VAL* 3.9 14.8 - - + -
9L ALA 2.9 16.2 + - - +
10L CYS* 3.6 6.0 - - - -
11L VAL* 3.0 24.9 + - - +
44L LEU* 4.0 28.3 - - + -
45L VAL* 3.7 20.9 - - + -
48L ALA* 3.6 25.4 - - + -
62L PRO* 3.7 26.2 - - + -
64L HIS 3.2 15.3 - - - +
65L PHE* 4.2 10.5 - + - -
66L ILE* 3.7 9.6 - - - +
82L PHE* 3.9 17.9 - - + -
83L LEU* 1.3 75.8 - - - +
85L ALA* 1.3 62.9 + - - +
138L LEU* 3.9 9.0 - - + -
141L ILE* 3.8 15.7 - - + -
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Residues in contact with ALA 85 (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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11L VAL 3.5 7.6 - - - +
62L PRO* 4.1 0.2 - - - +
63L GLN* 2.9 27.3 + - - +
64L HIS* 2.8 28.6 + - + +
66L ILE* 3.7 22.2 - - + +
84L PHE* 1.3 75.8 - - - +
86L ILE* 1.3 64.1 + - - +
87L GLU* 6.0 2.2 - - + -
130L TYR* 4.4 14.6 - - + -
135L ARG* 5.8 6.3 - - + +
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Residues in contact with ILE 86 (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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10L CYS* 3.6 29.6 - - + -
11L VAL 3.1 7.3 + - - +
12L VAL* 3.4 22.3 - - + +
13L HIS* 3.0 27.2 + - - +
52L LEU* 4.4 12.8 - - + -
60L ALA* 4.0 26.7 - - + +
61L GLN 3.8 8.5 - - - +
62L PRO* 3.7 20.4 - - + -
63L GLN* 3.6 15.9 - - - +
85L ALA* 1.3 78.2 - - - +
87L GLU* 1.3 64.3 + - - +
88L LEU* 4.2 14.4 - - + -
130L TYR* 5.6 0.4 - - - -
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Residues in contact with GLU 87 (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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144H PHE* 5.1 15.5 - - + -
145H ASN* 5.3 2.9 - - - +
13L HIS* 2.9 31.5 - - - +
14L ALA* 5.1 0.3 - - - -
63L GLN* 2.7 35.0 - - - +
85L ALA* 6.0 2.9 - - + -
86L ILE* 1.3 74.0 - - - +
88L LEU* 1.3 66.4 + - - +
89L GLU 4.3 0.5 + - - -
130L TYR* 2.4 33.2 + - + -
135L ARG* 4.5 18.3 + - - +
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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