Contacts of the helix formed by residues 120 - 132 (chain B) 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 SER 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASN* 5.2 0.7 + - - -
71B TRP* 4.1 20.4 - - - -
81B ARG* 5.2 2.4 + - - -
118B LEU* 3.2 11.6 - - - +
119B ARG* 1.3 83.0 - - - +
121B PRO* 1.3 75.4 - - - +
122B LEU* 3.0 24.7 + - - +
123B VAL* 3.2 24.7 + - - +
124B ALA 4.3 0.3 + - - -
158B SO4 5.6 4.8 + - - -
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Residues in contact with PRO 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TRP* 3.9 24.5 - - + +
74B PRO* 6.3 0.2 - - + -
118B LEU* 5.5 4.7 - - + -
120B SER* 1.3 88.9 - - - +
122B LEU* 1.3 54.9 + - - +
123B VAL 3.2 1.6 + - - -
124B ALA* 3.5 7.5 + - + +
125B GLU* 3.3 22.0 + - - +
89H GLU* 3.5 46.9 - - + +
144L PHE* 4.1 19.0 - - + -
145L ASN* 4.8 0.4 - - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B HIS* 3.7 35.0 - - + +
71B TRP* 3.9 44.0 - - + -
81B ARG* 3.5 32.8 + - + +
120B SER* 3.0 12.6 + - - +
121B PRO* 1.3 74.3 - - - +
123B VAL* 1.3 54.7 + - - +
125B GLU* 3.7 9.9 - - + -
126B SER* 2.6 36.6 + - - -
144L PHE* 3.4 30.5 - - + -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 5.0 3.8 - - + -
31B TRP 3.8 19.5 - - - +
32B ASN* 3.2 32.8 - - - +
33B GLN* 3.2 37.2 + - - +
81B ARG* 4.5 1.1 - - - +
112B ILE* 4.1 7.2 - - + -
118B LEU* 3.9 24.0 - - + -
120B SER* 3.2 30.0 + - - +
122B LEU* 1.3 75.2 - - - +
124B ALA* 1.3 67.9 + - - +
126B SER* 3.5 3.1 - - - -
127B ILE* 3.4 9.0 - - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 4.5 3.8 - - - -
113B LEU* 3.6 26.3 - - + +
118B LEU* 3.6 24.4 - - + +
121B PRO* 3.5 7.8 + - + +
123B VAL* 1.3 80.9 - - - +
125B GLU* 1.3 57.1 + - - +
127B ILE* 2.8 21.1 + - - +
128B ARG* 3.2 30.6 + - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ARG* 5.8 0.2 + - - -
69B HIS* 3.6 21.9 + - - +
121B PRO 3.3 15.0 + - - +
122B LEU* 4.0 11.0 - - + -
123B VAL 3.3 0.2 - - - -
124B ALA* 1.3 79.5 - - - +
126B SER* 1.3 56.6 + - - +
128B ARG* 3.2 20.2 + - - +
129B CYS* 2.9 28.6 + - - -
63H GLN* 6.1 0.9 - - - -
64H HIS* 4.2 5.2 - - - -
87H GLU* 4.0 12.6 - - - +
135H ARG* 2.7 39.1 + - - -
144L PHE* 3.4 35.3 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 4.3 3.2 - - - +
33B GLN* 3.3 27.9 + - - -
69B HIS* 4.8 2.5 - - - -
81B ARG* 2.9 20.6 + - - -
83B LEU* 3.4 29.5 - - - +
122B LEU 2.6 25.2 + - - -
123B VAL 3.5 0.7 - - - -
125B GLU* 1.3 75.8 - - - +
127B ILE* 1.3 57.5 + - - +
129B CYS* 3.3 3.8 + - - +
130B TYR* 2.9 27.5 + - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.6 8.1 - - + -
18B PHE* 4.1 25.8 - - + -
33B GLN* 3.7 15.9 - - + +
109B ALA* 3.9 28.5 - - + -
112B ILE* 3.9 31.4 - - + -
113B LEU* 3.7 17.3 - - + -
123B VAL 3.4 15.5 - - - +
124B ALA 2.8 12.5 + - - +
126B SER* 1.3 71.0 - - - +
128B ARG* 1.3 68.1 + - - +
130B TYR* 3.2 3.2 + - - +
131B GLN* 2.9 38.0 + - + +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 3.8 35.4 + - + +
124B ALA* 3.2 27.1 + - - +
125B GLU* 3.2 20.8 + - - +
127B ILE* 1.3 77.1 - - - +
129B CYS* 1.3 65.8 + - - +
131B GLN* 3.1 8.0 + - - +
132B SER* 3.0 21.0 + - - -
13H HIS* 4.0 11.3 + - - -
87H GLU* 3.4 38.0 + - - +
130H TYR* 3.5 19.2 + - - -
133H GLY 4.9 1.0 - - - +
135H ARG* 3.6 26.6 + - - +
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Residues in contact with CYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.8 16.6 - - + -
67B ARG* 3.9 6.5 - - - -
69B HIS* 3.6 29.4 - - - -
83B LEU* 4.4 2.0 - - + -
125B GLU* 2.9 16.8 + - - +
126B SER 3.6 8.1 - - - +
128B ARG* 1.3 77.8 - - - +
130B TYR* 1.3 64.3 + - - +
132B SER* 3.0 19.3 + - - -
133B GLY 3.8 1.4 + - - -
134B GLN* 3.7 27.2 + - - +
135H ARG* 3.1 26.2 - - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.6 28.5 - - + -
13B HIS* 3.1 25.0 + + + -
18B PHE* 3.6 24.7 - + + -
66B ILE* 4.2 21.2 - - + +
85B ALA* 4.5 11.7 - - + -
86B ILE 6.1 0.2 - - - -
87B GLU* 2.5 29.7 + - - -
126B SER 2.9 15.2 + - - +
127B ILE* 3.2 8.0 + - - +
129B CYS* 1.3 77.5 - - - +
131B GLN* 1.3 77.0 + - + +
133B GLY* 3.3 14.2 + - - -
134B GLN 4.6 3.2 - - - +
128C ARG* 4.2 8.9 - - - -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 4.6 6.6 - - + -
109B ALA* 3.6 30.6 - - - +
110B GLU* 5.3 2.7 + - - +
113B LEU* 4.2 11.6 - - - +
127B ILE* 2.9 28.8 + - + +
128B ARG* 3.1 5.8 + - - +
130B TYR* 1.3 87.9 - - + +
132B SER* 1.3 61.3 + - - +
133B GLY* 3.0 6.8 + - - -
132H SER 5.1 1.7 - - - +
133H GLY* 4.1 17.8 - - - +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG 3.0 9.5 + - - -
129B CYS 3.0 16.0 + - - -
131B GLN* 1.3 79.1 - - - +
133B GLY* 1.3 56.5 + - - +
134B GLN* 3.3 21.8 + - - +
131C GLN 5.2 1.4 - - - +
133H GLY 3.5 12.3 - - - +
134H GLN* 5.1 4.6 - - - +
135H ARG* 3.7 40.8 + - - +
136H TYR* 5.6 4.5 - - - -
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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