Contacts of the helix formed by residues 127 - 135 (chain B) in PDB entry 2G1N
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 PHE 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B SER* 2.3 28.6 + - - -
126B GLY* 1.3 74.7 - - - -
128B ILE* 1.3 65.2 + - - +
129B GLU* 3.1 9.7 + - - +
130B GLN* 3.2 4.6 + - - +
137B PRO* 3.9 0.4 - - - -
190B LEU* 3.6 21.5 - - + -
193B THR* 3.6 17.5 - - + -
194B GLY* 3.1 43.9 + - - -
195B VAL* 3.1 18.6 - - - -
196B TRP* 3.5 39.3 - + - -
324B ARG* 3.0 46.0 - - - +
327B ASN* 3.7 5.2 - - - -
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Residues in contact with ILE 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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127B PHE* 1.3 74.5 - - - +
129B GLU* 1.3 76.3 + - + +
131B ALA* 2.7 32.4 + - + +
134B ARG* 3.9 19.3 - - + +
135B VAL 3.5 9.9 - - - +
136B THR* 3.9 26.5 - - + +
137B PRO* 3.3 28.5 - - + +
140B ASP* 4.0 10.4 + - - +
324B ARG* 5.8 0.2 - - - +
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Residues in contact with GLU 129 (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 PHE* 3.1 5.1 - - - +
128B ILE* 1.3 97.3 + - + +
130B GLN* 1.3 63.1 + - + +
131B ALA 4.3 2.6 - - - +
193B THR* 3.8 17.3 - - - +
194B GLY* 3.7 35.3 + - - +
324B ARG* 5.8 0.9 + - - -
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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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35B GLY 5.2 9.8 + - - +
36B SER* 5.3 4.3 - - - -
37B SER* 3.3 19.4 + - - +
38B ASN* 4.5 1.4 - - - +
126B GLY* 5.8 1.3 - - - -
127B PHE 3.2 3.4 + - - +
128B ILE 3.0 0.8 - - - -
129B GLU* 1.3 78.2 - - - +
131B ALA* 1.3 68.4 + - - +
132B ILE* 3.5 9.7 + - - +
194B GLY 3.0 25.6 - - - +
195B VAL* 3.8 22.5 - - - +
303B PRO* 5.6 4.3 - - - +
304B THR* 3.4 26.6 + - - +
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Residues in contact with ALA 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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37B SER* 3.4 25.0 - - - +
38B ASN* 4.0 4.0 - - - +
128B ILE* 2.7 27.7 + - + +
129B GLU 4.3 2.8 - - - +
130B GLN* 1.3 83.0 - - - +
132B ILE* 1.3 59.8 - - - +
133B GLY 4.0 1.2 + - - -
134B ARG* 4.0 6.4 + - - -
135B VAL 3.3 29.6 - - - +
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Residues in contact with ILE 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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38B ASN* 3.2 31.8 + - - +
74B LEU* 4.3 18.7 - - + +
75B THR 3.0 30.5 - - - +
76B LEU* 3.3 23.6 - - + -
77B ARG* 4.8 3.1 - - + +
87B LEU* 5.6 0.2 - - - +
130B GLN 4.1 6.3 - - - +
131B ALA* 1.3 72.1 - - - +
133B GLY* 1.3 70.4 + - - +
134B ARG 3.0 2.1 + - - -
135B VAL* 3.4 13.9 + - - +
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Residues in contact with GLY 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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72B THR* 6.3 3.6 - - - -
74B LEU* 6.0 2.0 - - - -
87B LEU* 6.0 3.1 - - - -
131B ALA 4.0 0.2 + - - -
132B ILE* 1.3 74.9 - - - +
134B ARG* 1.3 87.4 + - - +
135B VAL* 2.9 14.2 + - - +
986B NAG 4.9 4.2 - - - -
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Residues in contact with ARG 134 (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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128B ILE* 3.9 18.1 - - + +
131B ALA* 4.0 12.2 + - - -
132B ILE 3.0 2.8 - - - -
133B GLY* 1.3 90.0 + - - +
135B VAL* 1.3 63.2 + - - +
136B THR* 3.5 2.9 + - - -
986B NAG 2.8 48.5 + - - -
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Residues in contact with VAL 135 (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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37B SER 4.7 2.8 - - - +
38B ASN* 4.8 10.5 - - - +
74B LEU* 5.6 0.7 - - + -
87B LEU* 3.5 31.2 - - + -
101B GLN* 4.6 0.2 - - - +
102B MET* 3.4 44.6 - - + +
128B ILE* 3.5 0.9 - - - +
131B ALA* 3.3 18.6 - - - +
132B ILE 3.4 20.3 + - - +
133B GLY 2.9 9.3 + - - +
134B ARG* 1.3 76.0 - - - +
136B THR* 1.3 71.2 + - - +
137B PRO* 3.3 5.4 - - - +
986B NAG 5.3 7.0 - - - -
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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