Contacts of the helix formed by residues 121 - 132 (chain F) 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 PRO 121 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71F TRP* 4.2 15.3 - - + +
74F PRO* 6.1 2.0 - - + -
118F LEU* 5.4 3.6 - - + -
120F SER* 1.4 86.7 - - - +
122F LEU* 1.3 64.6 + - - +
124F ALA* 3.0 20.5 + - + +
125F GLU* 3.3 8.7 + - - +
128F ARG* 4.9 1.6 + - - -
89I GLU* 4.0 21.1 - - - +
144K PHE* 4.3 8.8 - - + -
145K ASN* 3.6 24.7 - - - +
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F HIS* 3.6 39.9 - - + +
71F TRP* 3.7 43.1 - - + -
81F ARG* 3.8 33.7 - - + +
120F SER* 3.2 13.2 - - - +
121F PRO* 1.3 80.0 - - - +
123F VAL* 1.3 51.8 + - - +
125F GLU* 3.1 7.4 + - + +
126F SER* 2.5 40.6 + - - -
144K PHE* 3.6 25.5 - - + -
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Residues in contact with VAL 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL* 5.3 2.9 - - + -
31F TRP 3.9 10.5 - - - +
32F ASN* 3.6 35.9 - - - +
33F GLN* 3.1 43.3 + - - +
81F ARG* 4.8 1.3 - - - +
112F ILE* 4.4 8.1 - - + -
118F LEU* 4.2 22.4 - - + -
119F ARG 4.2 0.4 - - - +
120F SER* 3.1 34.3 - - - +
121F PRO 3.0 0.6 + - - -
122F LEU* 1.3 76.1 - - - +
124F ALA* 1.3 64.2 + - - +
126F SER* 3.3 4.3 - - - -
127F ILE* 3.4 6.1 + - - +
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Residues in contact with ALA 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ILE* 4.7 6.3 - - - +
113F LEU* 3.9 18.7 - - + +
118F LEU* 3.9 20.4 - - + +
121F PRO* 3.0 10.8 + - + +
123F VAL* 1.3 76.5 - - - +
125F GLU* 1.3 67.0 + - - +
126F SER 3.1 0.9 - - - -
127F ILE* 2.8 15.2 + - - +
128F ARG* 2.9 32.5 + - - +
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ARG* 5.2 0.9 + - - -
69F HIS* 3.6 10.1 + - - +
121F PRO 3.3 2.6 + - - -
122F LEU* 3.1 18.7 + - + +
124F ALA* 1.3 76.9 - - - +
126F SER* 1.3 65.2 + - - +
128F ARG* 2.9 22.2 + - - +
129F CYS* 2.7 39.5 + - - -
63I GLN* 5.2 1.4 + - - -
64I HIS* 4.6 5.8 - - - -
87I GLU* 4.6 4.4 - - + +
135I ARG* 2.7 44.3 + - - -
144K PHE* 3.3 42.6 - - + -
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Residues in contact with SER 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F VAL* 4.2 5.3 - - - +
33F GLN* 3.4 19.9 + - - -
69F HIS* 5.3 2.2 - - - -
81F ARG* 3.0 29.6 + - - -
83F LEU* 3.3 26.1 - - - +
122F LEU* 2.5 17.6 + - - +
123F VAL 3.3 11.7 - - - -
124F ALA 3.1 0.2 - - - -
125F GLU* 1.3 73.4 - - - +
127F ILE* 1.3 63.8 + - - +
129F CYS* 3.2 4.3 + - - +
130F TYR* 3.1 17.8 + - - +
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Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 4.9 5.2 - - + -
18F PHE* 4.2 26.5 - - + -
33F GLN* 3.2 31.6 - - + +
109F ALA* 3.9 27.6 - - + -
112F ILE* 3.5 34.3 - - + -
113F LEU* 4.0 16.8 - - + -
123F VAL 3.4 5.1 + - - +
124F ALA 2.8 13.1 + - - +
126F SER* 1.3 73.8 - - - +
128F ARG* 1.3 63.1 + - - +
130F TYR* 3.0 7.2 + - + +
131F GLN* 3.0 30.3 + - + +
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Residues in contact with ARG 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F LEU* 4.1 31.9 + - + +
121F PRO 4.9 1.6 + - - -
124F ALA* 2.9 15.3 + - - +
125F GLU* 2.9 48.7 + - - +
127F ILE* 1.3 75.9 - - - +
129F CYS* 1.3 61.3 + - - +
131F GLN* 3.2 22.4 + - - +
132F SER* 3.3 9.5 + - - -
13I HIS* 5.0 5.1 + - - -
87I GLU* 3.5 43.6 + - - +
130I TYR* 4.1 8.8 + - - -
133I GLY 4.9 1.0 - - - +
135I ARG* 3.8 29.9 + - - +
144K PHE* 5.1 3.0 - - - -
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Residues in contact with CYS 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ILE* 3.6 24.3 - - + +
67F ARG* 4.2 14.1 - - + -
69F HIS* 3.9 20.9 - - - -
83F LEU* 4.4 2.2 - - + -
125F GLU* 2.7 40.5 + - - +
126F SER 3.5 7.9 - - - +
128F ARG* 1.3 69.6 - - - +
130F TYR* 1.3 67.4 + - - +
132F SER* 3.3 18.9 + - - +
134F GLN 4.8 1.2 - - - +
135F ARG* 4.1 5.0 + - - -
135I ARG* 3.5 10.8 - - - +
139K GLU* 5.1 3.4 - - - -
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Residues in contact with TYR 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E HIS* 5.2 1.2 + - - -
137E PRO* 6.0 6.1 - - + -
11F VAL* 3.3 34.3 - - + -
13F HIS* 3.1 27.7 + + + -
18F PHE* 3.5 24.9 - + - -
66F ILE* 4.3 11.6 - - + +
85F ALA* 4.7 6.3 - - + -
86F ILE 5.6 0.2 - - - -
87F GLU* 2.3 33.0 + - - -
126F SER 3.1 10.5 + - - +
127F ILE* 3.0 13.1 + - - +
129F CYS* 1.3 73.8 - - - +
131F GLN* 1.3 71.0 + - + +
133F GLY* 3.1 14.0 + - - -
135F ARG* 2.7 51.3 + - - +
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Residues in contact with GLN 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PHE* 5.4 2.1 - - + -
109F ALA* 3.4 24.8 - - + +
110F GLU* 5.3 2.2 + - - -
113F LEU* 4.0 17.1 - - - +
127F ILE* 3.0 26.5 + - + +
128F ARG* 3.7 12.2 - - - +
129F CYS 3.1 0.4 - - - -
130F TYR* 1.3 91.7 - - + +
132F SER* 1.3 62.3 + - - +
133F GLY* 3.2 1.9 + - - -
132I SER 5.3 0.9 - - - +
133I GLY* 3.6 23.7 - - - +
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Residues in contact with SER 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLN* 3.6 13.7 + - - -
136E TYR* 5.4 2.8 - - - -
128F ARG 3.3 7.5 + - - -
129F CYS* 3.3 12.4 + - - -
130F TYR 3.1 1.2 + - - -
131F GLN* 1.3 78.8 - - - +
133F GLY* 1.3 58.9 + - - +
134F GLN* 2.7 40.0 + - - +
133I GLY 3.6 8.5 - - - -
134I GLN* 5.0 5.7 - - - +
135I ARG* 3.7 34.9 - - - +
136I TYR* 5.6 1.2 + - - -
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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