Contacts of the helix formed by residues 137 - 145 (chain A) in PDB entry 2G1Y
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER 4.1 20.9 - - - +
39A VAL* 6.2 0.2 - - + -
101A GLN* 3.7 1.1 - - - +
124A GLY 4.8 3.6 - - - +
126A GLY 3.9 13.2 - - - +
127A PHE 4.1 3.1 - - - -
128A ILE* 3.4 38.6 - - + +
131A ALA* 4.5 0.7 - - + -
135A VAL 3.1 8.7 - - - +
136A THR* 1.3 89.3 - - + +
138A ILE* 1.3 66.6 + - - +
139A PHE* 4.4 4.9 - - + +
140A ASP* 3.0 36.5 + - - +
141A ASN* 3.1 10.9 + - - -
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Residues in contact with ILE 138 (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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37A SER 5.2 0.2 + - - -
39A VAL* 4.1 9.8 - - + +
92A ILE* 4.3 17.5 - - + -
94A VAL* 3.6 31.2 - - + -
99A VAL* 3.8 18.2 - - + -
101A GLN* 3.1 31.2 + - + +
123A VAL* 3.7 33.7 - - + -
124A GLY 4.2 10.3 + - - +
125A MET* 4.4 8.3 - - + -
137A PRO* 1.3 73.1 - - - +
139A PHE* 1.3 69.4 + - - +
141A ASN* 3.2 2.4 + - - +
142A ILE* 3.0 33.3 + - + +
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Residues in contact with PHE 139 (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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124A GLY 5.1 0.6 + - - -
125A MET* 3.9 28.9 - - + +
126A GLY 5.8 1.3 - - - +
137A PRO* 3.2 4.4 - - + +
138A ILE* 1.3 83.1 - - + +
140A ASP* 1.3 65.2 + - - +
142A ILE* 3.3 7.5 + - + -
143A ILE* 3.0 56.9 + - + +
148A LEU* 3.7 29.2 - - + -
151A ASP 4.4 2.7 - - - -
152A VAL 3.9 22.2 - - - -
153A PHE* 3.5 41.5 - + + -
173A LEU* 4.5 12.8 - - + -
324A ARG* 3.6 28.7 - - + +
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Residues in contact with ASP 140 (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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127A PHE* 5.6 0.3 - - - -
128A ILE* 3.8 18.7 + - - +
136A THR* 3.9 13.0 - - + +
137A PRO* 3.0 34.2 + - - +
139A PHE* 1.3 76.2 - - - +
141A ASN* 1.3 65.2 + - - +
143A ILE* 3.1 10.6 + - - +
144A SER* 3.0 25.9 + - - -
324A ARG* 2.5 44.2 + - - -
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Residues in contact with ASN 141 (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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99A VAL* 4.8 7.6 - - + -
100A THR 3.7 15.9 - - - +
101A GLN* 2.9 30.0 + - - +
102A MET 5.1 0.5 + - - -
136A THR* 3.0 35.8 - - - +
137A PRO 3.1 5.4 + - - +
138A ILE 3.6 7.2 - - - +
139A PHE 3.2 0.2 - - - -
140A ASP* 1.3 77.6 - - - +
142A ILE* 1.3 62.5 + - - +
144A SER* 3.3 22.8 + - - -
145A GLN* 3.6 11.6 - - - +
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Residues in contact with ILE 142 (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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94A VAL* 5.0 5.8 - - + -
97A ILE* 3.5 36.6 - - + -
99A VAL* 3.6 24.5 - - + -
125A MET* 6.4 0.4 - - + -
138A ILE* 3.0 38.0 + - + +
139A PHE* 3.7 11.4 - - + +
140A ASP 3.3 0.2 - - - -
141A ASN* 1.3 75.2 - - - +
143A ILE* 1.3 63.7 + - - +
145A GLN* 3.1 19.9 + - - +
146A GLY 4.0 1.2 + - - -
147A VAL* 4.2 6.5 + - + +
148A LEU* 3.5 21.2 - - + +
173A LEU* 3.9 26.0 - - + -
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Residues in contact with ILE 143 (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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139A PHE* 3.0 54.4 + - + +
140A ASP* 3.4 9.6 - - - +
142A ILE* 1.3 77.2 - - - +
144A SER* 1.3 55.2 + - - +
146A GLY* 2.8 28.4 + - - -
147A VAL 5.9 0.2 - - - +
148A LEU* 4.2 12.6 - - + -
151A ASP* 3.0 37.7 - - + +
324A ARG* 4.0 18.6 - - + +
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Residues in contact with SER 144 (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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140A ASP* 3.0 14.5 + - - +
141A ASN* 3.4 19.8 + - - -
142A ILE 3.2 0.2 - - - -
143A ILE* 1.3 76.8 - - - +
145A GLN* 1.3 60.0 + - - +
146A GLY 3.2 1.3 + - - -
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Residues in contact with GLN 145 (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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97A ILE* 4.0 12.5 - - - +
98A THR 3.0 16.2 + - - +
99A VAL* 2.9 31.8 - - - +
141A ASN 3.6 12.4 - - - +
142A ILE 3.3 8.4 + - - +
143A ILE 2.9 1.2 + - - -
144A SER* 1.3 76.9 - - - +
146A GLY* 1.3 65.3 + - - +
147A VAL* 3.3 30.7 + - + +
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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