Contacts of the helix formed by residues 126 - 140 (chain B) in PDB entry 3GYQ
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 ILE 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B VAL* 3.8 1.6 - - + +
125B LYS* 1.3 74.8 - - + +
127B VAL* 1.3 65.7 + - + +
128B GLY* 3.8 11.7 - - - +
129B ASN* 2.9 44.8 + - - +
130B ILE* 3.2 10.7 + - - +
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Residues in contact with VAL 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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125B LYS 3.1 9.0 + - - +
126B ILE* 1.3 72.5 - - + +
128B GLY* 1.3 60.3 + - - +
130B ILE* 3.8 9.3 - - + +
131B GLY 2.8 25.8 + - - -
152B ILE* 4.2 20.0 - - + -
157B ASP* 5.3 1.1 - - - +
159B ARG* 3.6 67.3 - - + +
160B LEU* 4.4 8.0 - - + +
163B ALA* 3.6 11.2 - - + +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 3.0 9.5 + - - +
127B VAL* 1.3 85.0 - - - +
129B ASN* 1.3 63.2 + - - +
131B GLY* 4.0 0.3 - - - -
132B ALA* 3.2 25.3 + - - +
163B ALA* 4.5 8.7 - - - +
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Residues in contact with ASN 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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124B VAL* 4.1 15.0 - - + +
126B ILE* 2.9 36.9 + - - +
128B GLY* 1.3 76.4 - - - +
130B ILE* 1.3 59.2 + - - +
132B ALA* 3.5 5.0 + - - +
133B ILE* 2.9 36.7 + - - +
248B ASN* 4.1 22.0 + - - +
249B VAL* 4.0 23.7 - - + +
250B SER* 4.5 4.6 + - - -
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Residues in contact with ILE 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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121B LEU* 4.8 4.3 - - + -
124B VAL* 3.5 35.4 - - + +
125B LYS 4.1 14.1 - - - +
126B ILE 3.2 9.4 + - - +
127B VAL* 3.8 9.6 - - - +
129B ASN* 1.3 76.0 - - - +
131B GLY* 1.3 56.9 + - - +
133B ILE* 3.3 9.3 + - - +
134B VAL* 2.9 40.2 + - + +
147B LEU* 4.0 28.7 - - + -
150B SER* 4.2 4.9 - - - -
152B ILE* 4.2 23.8 - - + -
160B LEU* 3.7 19.7 - - + -
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Residues in contact with GLY 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 VAL 2.8 21.2 + - - -
129B ASN 3.3 0.2 - - - -
130B ILE* 1.3 73.3 - - - +
132B ALA* 1.3 61.8 + - - +
134B VAL* 3.0 14.4 + - - +
135B ARG* 3.1 11.1 + - - +
160B LEU* 4.0 1.5 - - - +
163B ALA* 3.4 20.2 - - - -
164B SER* 3.2 25.8 + - - -
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Residues in contact with ALA 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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248A ASN* 4.7 24.5 - - + +
251A VAL* 5.6 1.6 - - + -
128B GLY 3.2 18.1 + - - +
129B ASN* 3.9 3.8 - - - +
131B GLY* 1.3 74.4 - - - +
133B ILE* 1.3 56.3 + - - +
135B ARG* 3.3 13.0 + - - +
136B THR* 2.9 34.2 + - - +
163B ALA 3.8 4.4 + - - -
250B SER* 4.4 15.3 - - - +
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Residues in contact with ILE 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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119B VAL* 4.4 4.9 - - + -
121B LEU* 3.6 35.7 - - + -
124B VAL* 4.8 2.0 - - + -
129B ASN* 2.9 28.5 + - + +
130B ILE 3.5 4.5 - - - +
132B ALA* 1.3 75.0 - - - +
134B VAL* 1.3 58.0 + - + +
136B THR* 4.5 0.9 - - - -
137B SER* 2.8 43.0 + - - +
145B ILE* 4.1 9.2 - - + -
249B VAL* 3.9 31.4 - - + +
250B SER* 3.8 18.2 - - - -
253B LEU* 3.3 27.7 - - + +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 2.9 31.2 + - + +
131B GLY 3.0 8.5 + - - +
133B ILE* 1.3 77.0 - - - +
135B ARG* 1.3 62.5 + - - +
137B SER* 3.8 1.7 - - - -
138B LEU* 3.1 22.3 + - - +
145B ILE* 3.7 19.1 - - + -
160B LEU* 5.0 0.2 - - + -
164B SER* 3.7 17.0 - - - +
167B TYR* 3.6 33.4 - - + +
168B VAL* 4.0 9.0 - - + -
171B LEU* 3.9 13.3 - - + +
173B VAL* 4.5 13.0 - - + -
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Residues in contact with ARG 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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246A SER* 2.9 29.2 + - - +
247A LEU 4.2 1.0 - - - -
248A ASN* 4.1 20.9 - - + +
270A SAM 2.6 49.3 + - - -
131B GLY 3.1 9.3 + - - +
132B ALA* 3.3 11.3 + - - +
134B VAL* 1.3 77.7 - - - +
136B THR* 1.3 56.8 + - - +
138B LEU* 3.3 7.4 + - - +
139B ALA* 3.0 30.9 + - - +
163B ALA 4.6 4.7 - - - -
164B SER 3.3 22.2 - - - +
165B ARG* 3.7 30.9 - - - +
167B TYR* 4.0 16.2 - - + -
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Residues in contact with THR 136 (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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247A LEU* 5.2 7.2 - - + +
248A ASN* 5.2 4.5 + - - +
251A VAL* 3.8 28.8 - - + +
132B ALA* 2.9 17.5 + - - +
133B ILE 4.0 3.4 - - - -
135B ARG* 1.3 75.8 - - - +
137B SER* 1.3 64.2 + - - +
139B ALA* 3.3 4.4 + - - -
140B LEU* 3.0 38.8 + - + +
250B SER* 4.9 1.6 + - - +
253B LEU* 4.2 10.8 - - + -
254B GLY* 3.8 31.6 - - - +
257B LEU* 4.6 2.0 - - + -
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Residues in contact with SER 137 (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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119B VAL* 3.5 16.1 - - - +
133B ILE* 2.8 24.7 + - - +
134B VAL 3.8 1.1 - - - -
136B THR* 1.3 75.6 - - - +
138B LEU* 1.3 60.0 - - - +
140B LEU 3.5 0.5 + - - -
141B GLY 3.3 3.8 + - - -
142B ALA* 2.8 44.6 + - - +
145B ILE* 3.5 25.9 - - - +
171B LEU* 4.2 3.6 - - - -
253B LEU* 3.5 8.0 - - - +
257B LEU* 3.7 10.7 - - - +
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Residues in contact with LEU 138 (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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241A MET* 3.8 9.2 - - - +
245A GLU* 4.6 7.2 - - - +
42B HIS* 4.2 22.2 - - + +
114B ARG* 5.7 3.4 - - - +
134B VAL 3.1 17.9 + - - +
135B ARG 3.6 4.5 - - - +
136B THR 3.3 0.2 - - - -
137B SER* 1.3 78.4 - - - +
139B ALA* 1.3 62.9 + - - +
140B LEU 3.4 0.5 + - - -
141B GLY* 3.5 7.6 + - - -
142B ALA 5.0 3.0 - - - +
167B TYR* 3.3 42.6 - - + -
170B SER* 3.7 34.8 - - - +
171B LEU* 4.2 17.4 - - + +
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Residues in contact with ALA 139 (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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240A MET* 3.4 6.9 - - - +
241A MET* 2.9 28.5 + - - +
245A GLU* 3.6 28.7 - - + +
246A SER 5.1 3.1 - - - +
247A LEU* 3.7 28.7 - - + -
135B ARG 3.0 16.9 + - - +
136B THR 3.3 2.0 + - - +
138B LEU* 1.3 77.3 - - + +
140B LEU* 1.3 59.0 + - - +
141B GLY 3.4 0.2 - - - -
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Residues in contact with LEU 140 (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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238A ILE* 5.2 2.9 - - + -
239A PRO 3.7 22.2 - - - +
240A MET* 4.4 7.0 - - + -
241A MET* 4.0 0.4 - - - -
247A LEU* 4.6 11.4 - - + -
255A ILE* 4.5 7.6 - - + -
136B THR* 3.0 32.6 + - + +
139B ALA* 1.3 85.2 - - + +
141B GLY* 1.3 60.0 + - - +
142B ALA 3.6 2.4 + - - -
254B GLY* 3.4 26.7 - - - +
257B LEU* 3.6 29.0 - - + +
258B HIS* 3.8 10.5 - - - +
261B ILE* 3.3 30.3 - - + +
264B ASN* 4.2 10.7 - - - +
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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