Contacts of the helix formed by residues 124 - 133 (chain B) in PDB entry 1C7G
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 THR 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B TYR* 4.3 11.1 - - + -
123B PHE* 1.3 91.7 - - + +
125B THR* 1.3 76.0 + - - +
127B ARG* 4.0 1.7 - - - +
128B PHE* 3.1 24.7 + - - +
186B LEU* 5.9 3.1 - - + +
381B ARG* 5.6 8.1 - - - +
283D VAL* 6.1 0.3 - - - +
284D VAL* 6.2 0.2 - - - -
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 3.4 55.9 - - + +
103B GLU* 3.1 12.7 + - - -
123B PHE* 3.1 19.8 - - + -
124B THR* 1.3 89.5 + - - +
126B THR* 1.3 63.9 + - - +
128B PHE* 3.5 6.2 + - - +
129B HIS* 3.2 30.9 + - - -
1000B PLP 4.3 1.0 + - - -
283D VAL* 4.3 7.9 - - + +
284D VAL* 4.6 11.7 - - + -
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU* 3.1 36.6 - - - +
107B SER* 4.7 1.4 + - - -
122B TYR* 5.3 2.3 - - - +
123B PHE* 3.2 42.8 + - + +
125B THR* 1.3 74.2 + - - +
127B ARG* 1.3 66.2 + - - +
129B HIS* 3.5 3.1 + - - +
130B GLN* 3.2 36.8 + - - +
179B CYS* 4.8 8.4 - - - -
214B ASP* 3.8 13.4 + - - +
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Residues in contact with ARG 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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122B TYR* 3.6 48.0 + - + -
123B PHE 3.0 15.7 + - - +
124B THR* 4.1 2.7 - - - +
126B THR* 1.3 78.7 + - - +
128B PHE* 1.3 64.5 + - - +
130B GLN* 3.0 24.6 + - - +
131B GLU* 2.7 65.2 + - - +
137B PHE* 3.6 39.2 + - + +
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Residues in contact with PHE 128 (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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124B THR 3.1 18.8 + - - +
125B THR* 3.5 6.5 - - - +
126B THR 3.2 0.2 - - - -
127B ARG* 1.3 78.0 - - - +
129B HIS* 1.3 100.4 + + - +
130B GLN 2.9 0.7 + - - -
131B GLU* 3.0 7.8 + - - +
132B LYS* 2.6 62.8 + - + +
281D LEU* 5.7 4.5 - - + -
284D VAL* 3.9 38.6 - - + -
285D TYR* 4.5 8.7 - + - -
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 3.8 8.7 + - + +
103B GLU* 4.0 9.4 - - + +
104B ASN* 3.5 40.0 - - + +
107B SER* 3.4 20.7 - - - +
125B THR 3.2 24.7 + - - +
126B THR 3.9 3.1 - - - +
128B PHE* 1.3 100.8 - + - +
130B GLN* 1.3 62.3 + - - +
132B LYS* 3.2 19.3 + - - +
133B ASN* 2.6 28.5 + - - +
284D VAL 2.9 28.7 + - - -
285D TYR* 4.0 11.9 - + - -
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Residues in contact with GLN 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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107B SER* 3.6 2.7 + - - +
111B ILE* 3.6 15.9 - - + +
117B VAL* 3.7 25.7 - - + +
122B TYR* 5.6 0.6 - - - +
126B THR* 3.2 28.0 + - - +
127B ARG* 3.0 25.3 + - - +
128B PHE 3.0 0.2 - - - -
129B HIS* 1.3 81.1 - - - +
131B GLU* 1.3 64.8 + - + +
133B ASN* 3.2 6.4 + - - -
135B ALA* 3.3 23.8 + - + +
137B PHE* 3.7 31.2 - - + +
177B TYR* 3.9 19.9 + - - +
179B CYS* 4.1 14.9 - - - +
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Residues in contact with GLU 131 (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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127B ARG* 2.7 59.6 + - + +
128B PHE* 3.7 7.0 - - - +
130B GLN* 1.3 72.7 - - + +
132B LYS* 1.3 58.2 + - - +
133B ASN 2.9 2.5 - - - -
134B GLY* 2.7 27.0 + - - -
135B ALA 3.5 22.6 + - - +
136B THR* 5.3 0.2 - - - -
137B PHE* 4.3 8.1 + - - +
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Residues in contact with LYS 132 (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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104B ASN* 3.0 26.0 + - - -
108B GLN* 3.9 10.5 - - - +
128B PHE* 2.6 43.0 + - + +
129B HIS* 3.2 26.5 + - - +
131B GLU* 1.3 73.5 - - - +
133B ASN* 1.3 83.0 + - - +
134B GLY 3.5 2.3 + - - -
285D TYR* 3.7 21.3 - - - +
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Residues in contact with ASN 133 (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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107B SER* 3.4 26.1 - - - +
108B GLN* 3.4 30.3 + - - +
111B ILE* 3.4 17.1 - - + +
113B PRO* 4.3 11.2 - - - +
129B HIS 2.6 24.0 + - - +
130B GLN 3.2 5.9 + - - +
131B GLU 2.9 1.4 - - - -
132B LYS* 1.3 102.4 + - - +
134B GLY* 1.3 62.6 + - - +
135B ALA 3.8 0.7 - - - -
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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