Contacts of the helix formed by residues 124 - 131 (chain A) in PDB entry 2G7F
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 GLY 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ARG* 3.0 21.1 + - - -
75A ARG 2.8 15.1 + - - -
77A GLU* 3.2 35.3 - - - +
122A ALA 3.2 1.4 + - - -
123A ILE* 1.3 70.5 - - - +
125A GLU* 1.3 55.4 + - - +
127A ASN* 3.2 1.3 + - - -
128A GLY 2.8 27.4 + - - -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 2.7 31.6 + - - +
66A VAL* 3.7 2.1 - - - -
67A ARG* 2.9 31.9 + - - +
68A LYS* 2.9 12.6 + - - +
69A ASN* 2.8 37.8 + - + +
72A ARG* 3.2 16.1 + - + +
73A ALA* 3.8 18.0 - - - +
123A ILE* 3.4 1.6 - - + +
124A GLY* 1.3 73.5 - - - +
126A VAL* 1.3 58.2 + - - +
128A GLY* 3.8 0.4 - - - -
129A ASN* 2.9 51.0 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.8 22.4 - - + -
44A CYS* 4.4 9.6 - - - -
64A TYR* 3.6 34.8 - - + +
123A ILE* 3.1 18.0 + - + +
125A GLU* 1.3 75.3 - - - +
127A ASN* 1.3 55.7 + - - +
129A ASN* 3.3 5.0 + - - +
130A ARG* 2.8 34.7 + - - +
146A TYR* 4.3 14.4 - - + +
151A MET* 3.7 34.5 - - + -
153A VAL* 5.2 0.6 - - + +
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Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 5.6 0.7 - - - -
72A ARG* 4.0 4.9 - - - +
77A GLU* 2.9 34.2 + - + +
78A TRP 4.1 12.5 + - - -
79A GLU* 2.7 14.6 - - - +
122A ALA* 4.5 11.5 - - + +
123A ILE 3.1 12.4 + - - +
124A GLY 3.5 7.4 - - - +
126A VAL* 1.3 74.8 - - - +
128A GLY* 1.3 63.3 + - - +
130A ARG* 4.0 4.6 - - - +
131A SER* 3.1 19.1 + - - -
301A MG 2.1 35.1 - - - -
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG* 3.5 33.2 - - - +
124A GLY 2.8 17.0 + - - -
125A GLU* 3.9 1.6 - - - -
127A ASN* 1.3 72.7 - - - +
129A ASN* 1.3 63.3 + - - +
131A SER* 3.2 16.5 + - - -
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 3.3 28.9 + - - +
69A ASN* 6.0 1.2 - - - +
125A GLU* 2.9 35.8 + - - +
126A VAL 3.8 2.5 - - - +
128A GLY* 1.3 73.0 - - - +
130A ARG* 1.3 63.0 + - - +
131A SER* 3.3 2.9 + - - -
133A PHE* 3.6 9.5 - - - -
146A TYR* 2.8 37.3 + - - +
153A VAL* 3.5 17.4 - - + +
155A PHE* 3.7 25.0 - - + -
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.7 0.6 + - - +
79A GLU* 2.8 38.1 + - - +
80A HIS 3.4 9.1 + - - -
81A VAL 2.9 18.2 + - - -
83A PRO* 3.5 15.6 - - - +
126A VAL* 2.8 23.7 + - + +
127A ASN 4.0 2.9 - - - +
129A ASN* 1.3 72.4 - - - +
131A SER* 1.3 76.4 + - - +
133A PHE* 3.0 53.1 + - - -
135A PHE* 3.2 33.7 - - + -
151A MET* 4.0 26.2 - - + -
153A VAL* 4.2 8.9 - - + +
160A ALA* 4.0 12.3 - - + -
174A TYR* 3.2 18.2 + - - -
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PRO* 4.5 4.0 - - - +
127A ASN 3.1 12.2 + - - -
128A GLY 3.2 11.7 + - - -
129A ASN 3.8 7.4 - - - -
130A ARG* 1.3 91.6 + - - +
132A ASN* 1.3 74.2 + - - +
133A PHE* 3.9 17.5 - - - -
158A ARG* 4.8 2.3 + - - -
301A MG 4.1 12.0 - - - -
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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