Contacts of the helix formed by residues 122 - 131 (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 LEU 122 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B PHE* 3.3 31.6 - - + -
69L HIS* 3.4 40.2 - - + +
71L TRP* 3.7 40.8 - - + +
81L ARG* 3.3 29.1 + - + +
120L SER* 2.8 11.7 + - - +
121L PRO* 1.3 76.2 - - - +
123L VAL* 1.3 58.4 + - - +
124L ALA 3.2 1.1 - - - -
125L GLU* 3.8 11.6 - - + +
126L SER* 2.7 34.0 + - - -
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Residues in contact with VAL 123 (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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20L VAL* 4.5 7.2 - - + -
31L TRP 4.2 0.4 - - - +
32L ASN* 3.6 23.8 - - - +
33L GLN* 2.8 61.4 + - - +
81L ARG* 5.4 0.9 - - - +
112L ILE* 4.0 5.1 - - + +
118L LEU* 4.2 20.6 - - + -
119L ARG* 3.9 10.5 - - + +
120L SER* 2.9 32.9 + - - +
122L LEU* 1.3 76.5 - - - +
124L ALA* 1.3 57.4 + - - +
125L GLU 3.1 4.6 + - - -
126L SER 3.5 3.3 + - - -
127L ILE* 3.7 9.4 + - - +
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Residues in contact with ALA 124 (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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112L ILE* 4.2 17.5 - - - +
113L LEU* 4.6 10.2 - - - +
118L LEU* 3.7 22.1 - - + +
120L SER 4.1 0.2 + - - -
121L PRO* 3.5 13.5 + - + +
122L LEU 3.2 0.2 - - - -
123L VAL* 1.3 76.6 - - - +
125L GLU* 1.3 57.0 + - - +
127L ILE* 4.4 3.8 - - - -
128L ARG* 2.9 42.6 + - - +
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Residues in contact with GLU 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 3.7 31.7 - - + -
63G GLN* 5.4 0.7 + - - -
64G HIS* 4.3 6.1 + - - -
87G GLU* 4.5 7.4 - - - +
135G ARG* 2.9 36.5 + - - -
67L ARG* 5.3 1.2 + - - -
69L HIS* 3.7 12.6 + - - +
121L PRO 3.4 18.6 - - - +
122L LEU* 3.8 20.9 - - + -
124L ALA* 1.3 74.6 - - - +
126L SER* 1.3 62.9 + - - +
127L ILE 3.2 1.6 - - - -
128L ARG* 3.3 9.3 + - - +
129L CYS* 2.9 44.4 + - - -
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Residues in contact with SER 126 (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* 4.1 7.0 - - - +
33L GLN* 3.3 24.0 + - - -
69L HIS* 5.2 1.7 - - - -
81L ARG* 2.8 20.8 + - - -
83L LEU* 3.6 30.2 - - - +
122L LEU 2.7 22.3 + - - -
125L GLU* 1.3 76.4 - - - +
127L ILE* 1.3 58.8 + - - +
129L CYS* 3.2 4.0 + - - +
130L TYR* 2.9 27.0 + - - +
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Residues in contact with ILE 127 (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* 4.3 12.6 - - + -
18L PHE* 3.9 35.9 - - + -
33L GLN* 4.1 13.2 - - + +
109L ALA* 3.8 23.6 - - + +
112L ILE* 4.1 21.1 - - + -
113L LEU* 3.8 24.5 - - + -
123L VAL 3.7 15.0 + - - +
124L ALA 4.8 3.1 - - - +
125L GLU 3.2 0.2 - - - -
126L SER* 1.3 75.1 - - - +
128L ARG* 1.3 57.6 + - - +
129L CYS 2.9 4.7 + - - -
130L TYR* 3.2 2.8 + - + +
131L GLN* 2.9 42.2 + - + +
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Residues in contact with ARG 128 (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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13G HIS* 3.5 11.1 + - - -
87G GLU* 2.9 37.6 + - - +
88G LEU 5.5 2.8 + - - -
130G TYR* 2.9 28.8 + - - -
133G GLY 4.6 1.2 - - - +
135G ARG* 3.1 48.9 + - - +
113L LEU* 3.4 41.2 + - + +
121L PRO 5.8 0.2 + - - -
124L ALA* 2.9 39.2 + - - +
125L GLU* 3.3 10.5 + - - +
127L ILE* 1.3 76.8 - - - +
129L CYS* 1.3 60.5 + - - +
131L GLN* 4.0 7.6 - - - +
132L SER 3.7 8.5 + - - -
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Residues in contact with CYS 129 (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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64G HIS* 5.5 0.9 - - - -
135G ARG* 3.9 9.2 - - - +
66L ILE* 3.9 19.7 - - + -
67L ARG* 3.9 26.2 - - - -
69L HIS* 3.9 9.9 - - - -
83L LEU* 4.2 2.0 - - + -
125L GLU* 2.9 35.7 + - - -
126L SER* 3.3 11.4 - - - +
127L ILE 2.9 0.8 - - - -
128L ARG* 1.3 73.8 - - - +
130L TYR* 1.3 63.8 + - - +
131L GLN 3.1 1.1 - - - -
132L SER* 2.5 31.1 + - - -
134L GLN* 4.4 11.1 + - - +
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Residues in contact with TYR 130 (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* 3.3 31.4 - - + -
13L HIS* 2.5 35.8 + + + -
18L PHE* 4.0 14.1 - + + -
66L ILE* 4.0 19.6 - - + +
85L ALA* 4.4 12.6 - - + -
86L ILE 5.6 0.4 - - - -
87L GLU* 2.4 33.8 + - + -
126L SER 2.9 15.9 + - - +
127L ILE* 3.8 5.6 - - - +
129L CYS* 1.3 75.2 - - - +
131L GLN* 1.3 69.6 + - + +
132L SER 3.2 0.2 - - - -
133L GLY* 3.1 20.1 + - - -
134L GLN 4.6 2.5 + - - +
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Residues in contact with GLN 131 (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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132G SER 5.1 3.4 - - - +
133G GLY* 2.9 30.7 - - - +
134G GLN* 4.8 0.5 - - - -
18L PHE* 3.2 27.0 - - + -
109L ALA* 3.3 26.7 - - - +
110L GLU* 5.4 1.0 - - - +
113L LEU* 5.0 4.3 - - - +
127L ILE* 2.9 25.9 + - + +
128L ARG* 4.1 6.2 - - - +
129L CYS 3.1 0.4 - - - -
130L TYR* 1.3 86.5 - - + +
132L SER* 1.3 62.7 + - - +
133L GLY 3.0 0.9 - - - -
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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