Contacts of the helix formed by residues 121 - 132 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.8 8.2 - - + -
145C ASN* 4.2 16.8 - - - +
71G TRP* 3.2 34.5 - - + -
74G PRO* 6.0 1.1 - - + -
119G ARG 4.7 0.7 - - - +
120G SER* 1.3 90.3 - - - +
122G LEU* 1.3 59.0 + - - +
123G VAL 3.3 1.1 + - - -
124G ALA* 4.2 4.8 + - + +
125G GLU* 3.6 19.8 + - - +
128G ARG* 5.0 1.9 + - - -
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.7 21.8 - - + -
33G GLN* 4.7 0.7 - - - -
69G HIS* 3.6 41.7 - - + +
71G TRP* 3.9 43.7 - - + +
81G ARG* 3.7 39.0 - - + +
120G SER* 2.8 14.3 + - - +
121G PRO* 1.3 79.3 - - - +
123G VAL* 1.3 51.3 + - - +
125G GLU* 3.7 2.0 - - + +
126G SER* 2.7 42.5 + - - -
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Residues in contact with VAL 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G VAL* 5.6 2.7 - - + -
31G TRP* 4.0 11.2 - - + +
32G ASN* 3.4 34.5 - - - +
33G GLN* 3.3 33.8 + - - +
81G ARG* 5.0 0.4 - - - +
112G ILE* 4.2 9.4 - - + -
118G LEU* 4.1 24.9 - - + -
119G ARG 4.1 0.2 - - - +
120G SER* 3.0 33.2 + - - +
122G LEU* 1.3 75.0 - - - +
124G ALA* 1.3 65.6 + - - +
126G SER* 3.4 0.3 - - - -
127G ILE* 3.2 19.6 + - - +
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Residues in contact with ALA 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G ILE* 5.2 1.8 - - - -
113G LEU* 3.9 22.8 - - + +
118G LEU* 4.1 21.0 - - + +
120G SER 4.5 1.0 + - - +
121G PRO* 4.2 4.7 + - + +
123G VAL* 1.3 75.7 - - - +
125G GLU* 1.3 68.4 + - - +
127G ILE* 2.8 5.5 + - - +
128G ARG* 2.8 46.3 + - - +
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Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.4 38.2 - - + -
67G ARG* 5.6 1.4 + - - -
69G HIS* 3.7 21.4 + - + +
121G PRO 3.6 18.3 + - - +
122G LEU* 3.7 6.5 - - + +
123G VAL 3.4 0.4 - - - -
124G ALA* 1.3 76.3 - - - +
126G SER* 1.3 53.1 + - - +
128G ARG* 2.9 33.9 + - - +
129G CYS* 2.5 48.8 + - - +
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Residues in contact with SER 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 4.2 2.9 - - - +
33G GLN* 3.4 20.1 + - - -
69G HIS* 5.0 4.0 + - - -
81G ARG* 3.2 22.9 + - - -
83G LEU* 3.3 27.4 - - - +
122G LEU 2.7 26.1 + - - -
123G VAL 3.4 7.2 - - - -
125G GLU* 1.3 72.9 - - - +
127G ILE* 1.3 62.2 + - - +
129G CYS* 3.3 4.7 + - - +
130G TYR* 3.0 22.5 + - - +
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Residues in contact with ILE 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 5.2 3.8 - - + -
18G PHE* 4.3 31.0 - - + -
33G GLN* 3.1 32.3 - - - +
109G ALA* 4.6 7.9 - - + -
112G ILE* 4.0 28.7 - - + -
113G LEU* 3.7 22.0 - - + -
123G VAL 3.2 8.3 + - - +
124G ALA 2.8 10.9 + - - +
126G SER* 1.3 74.5 - - - +
128G ARG* 1.3 59.4 + - - +
130G TYR* 3.0 4.8 + - - +
131G GLN* 2.8 56.5 + - + +
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Residues in contact with ARG 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 5.3 2.6 - - - -
113G LEU* 4.5 21.9 + - + +
121G PRO 5.0 2.0 + - - -
124G ALA* 2.8 32.4 + - - +
125G GLU* 3.2 47.4 + - - +
127G ILE* 1.3 68.8 - - - +
129G CYS* 1.3 66.2 + - - +
131G GLN* 3.8 15.3 - - - +
132G SER* 3.0 23.9 + - - -
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Residues in contact with CYS 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ILE* 4.1 17.5 - - + -
67G ARG* 4.0 15.9 - - - -
69G HIS* 3.6 33.0 - - - -
83G LEU* 4.2 5.6 - - + -
125G GLU* 2.5 30.4 + - - +
126G SER 3.5 6.7 - - - +
128G ARG* 1.3 73.4 - - - +
130G TYR* 1.3 58.7 + - - +
132G SER* 2.5 27.7 + - - -
133G GLY 4.0 0.2 + - - -
134G GLN* 4.0 17.6 + - - +
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Residues in contact with TYR 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 3.6 28.9 - - + -
13G HIS* 3.3 16.8 + + + -
18G PHE* 3.5 30.1 - + - -
66G ILE* 4.4 20.9 - - + -
85G ALA* 4.6 11.7 - - + -
87G GLU* 3.2 18.1 + - - -
126G SER 3.0 13.1 + - - +
127G ILE* 3.0 8.5 + - - +
129G CYS* 1.3 75.5 - - - +
131G GLN* 1.3 69.5 + - + +
133G GLY* 2.9 22.3 + - - -
134G GLN 4.4 3.8 + - - +
135G ARG* 6.3 1.1 - - - -
113L LEU* 4.4 7.9 - - + +
128L ARG* 2.9 34.7 + - - -
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Residues in contact with GLN 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G PHE* 4.9 4.0 - - + -
109G ALA* 3.3 29.3 - - - +
113G LEU* 3.8 14.3 - - - +
127G ILE* 2.8 36.3 + - + +
128G ARG* 3.8 12.1 - - - +
130G TYR* 1.3 85.3 - - + +
132G SER* 1.3 62.0 + - - +
133G GLY* 2.9 7.5 + - - -
110L GLU* 5.7 0.7 - - - +
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Residues in contact with SER 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ARG 3.0 13.5 + - - -
129G CYS* 2.5 23.6 + - - -
131G GLN* 1.3 76.2 - - - +
133G GLY* 1.3 59.6 + - - +
134G GLN* 3.1 24.9 + - - +
131L GLN* 5.1 3.5 - - - +
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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