Contacts of the helix formed by residues 248 - 259 (chain A) 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 ASN 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ASN* 3.8 20.9 + - - +
246A SER 4.2 0.2 + - - -
247A LEU* 1.3 73.1 - - - +
249A VAL* 1.3 62.2 + - - +
250A SER* 2.7 43.6 + - - -
251A VAL* 3.2 17.5 + - + +
252A SER* 2.8 30.1 + - - -
270A SAM 4.2 15.5 + - - -
132B ALA* 4.7 19.2 - - + +
135B ARG* 4.1 20.9 - - + +
136B THR* 5.2 4.2 + - - +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.5 0.4 - - + -
124A VAL* 4.4 13.7 - - + -
129A ASN* 3.6 38.1 - - + +
133A ILE* 3.8 17.7 - - + -
217A PHE* 4.2 18.5 - - + -
218A GLY 4.0 18.6 - - - +
219A SER* 5.9 0.9 - - - -
247A LEU 3.7 1.4 + - - -
248A ASN* 1.3 76.4 + - - +
250A SER* 1.3 59.3 + - - +
252A SER* 3.4 2.3 + - - -
253A LEU* 3.0 27.4 + - + +
270A SAM 3.8 29.9 + - + +
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Residues in contact with SER 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASN* 4.5 7.3 + - - -
132A ALA* 4.4 20.6 - - - +
133A ILE* 3.8 26.5 - - - -
136A THR* 4.8 1.7 + - - -
248A ASN* 2.7 26.9 + - - -
249A VAL* 1.3 75.6 - - - +
251A VAL* 1.3 61.2 + - - +
253A LEU* 3.3 4.6 + - - +
254A GLY* 2.9 25.3 + - - -
250B SER* 4.8 4.3 + - - -
251B VAL* 4.0 19.1 - - - +
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Residues in contact with VAL 251 (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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247A LEU* 4.2 15.0 - - + -
248A ASN* 3.2 22.3 + - + +
250A SER* 1.3 84.7 + - - +
252A SER* 1.3 65.7 + - - +
254A GLY* 3.3 1.6 + - - +
255A ILE* 3.1 29.0 + - + +
132B ALA* 5.6 1.8 - - + -
136B THR* 3.8 24.7 - - + +
250B SER* 3.8 31.0 - - - +
251B VAL* 4.5 7.9 - - - +
254B GLY* 4.1 24.2 - - - -
255B ILE* 5.8 0.2 - - - +
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Residues in contact with SER 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 4.0 6.4 - - - -
238A ILE* 3.6 18.1 - - - +
247A LEU* 3.2 17.0 - - - +
248A ASN 2.8 19.2 + - - -
249A VAL 3.6 2.5 - - - -
251A VAL* 1.3 78.2 - - - +
253A LEU* 1.3 61.9 + - - +
255A ILE 3.5 0.3 + - - -
256A ALA* 3.0 23.2 + - - +
270A SAM 3.2 45.6 + - - -
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Residues in contact with LEU 253 (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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119A VAL* 3.6 27.8 - - + -
121A LEU* 5.7 0.4 - - + -
133A ILE* 3.4 50.7 - - + +
136A THR* 4.0 13.7 - - + -
137A SER* 3.7 6.1 - - - +
217A PHE* 3.6 35.6 - - + -
249A VAL 3.0 16.6 + - - +
250A SER* 3.5 5.2 - - - +
252A SER* 1.3 74.5 - - - +
254A GLY* 1.3 64.7 + - - +
256A ALA* 3.0 2.9 + - - +
257A LEU* 2.9 34.5 + - + +
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Residues in contact with GLY 254 (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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136A THR* 3.6 23.1 - - - -
140A LEU* 3.7 6.0 - - - +
250A SER 2.9 14.0 + - - -
251A VAL 3.3 3.1 + - - -
253A LEU* 1.3 76.8 - - - +
255A ILE* 1.3 56.8 + - - +
258A HIS* 2.8 31.1 + - - +
251B VAL* 4.1 12.3 - - - -
255B ILE* 3.8 7.2 - - - +
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Residues in contact with ILE 255 (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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203A VAL* 4.4 4.0 - - + -
238A ILE* 3.9 20.9 - - + -
247A LEU* 3.9 28.5 - - + -
251A VAL* 3.1 18.1 + - + +
252A SER 3.8 4.0 - - - +
254A GLY* 1.3 74.8 - - - +
256A ALA* 1.3 62.8 + - - +
258A HIS* 3.3 7.6 + - - +
259A GLU* 3.1 22.7 + - - +
140B LEU* 4.5 4.0 - - + -
254B GLY 3.8 32.1 - - - +
255B ILE* 4.3 5.6 - - + +
258B HIS* 3.7 42.0 - - + +
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Residues in contact with ALA 256 (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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195A LEU* 3.5 26.2 - - + -
203A VAL* 4.0 12.1 - - + -
206A LEU* 4.4 5.5 - - + +
215A LEU* 4.4 9.9 - - + -
217A PHE* 3.8 11.4 - - + -
252A SER 3.0 15.7 + - - +
253A LEU 3.0 8.0 + - - +
255A ILE* 1.3 79.2 - - - +
257A LEU* 1.3 63.0 + - - +
259A GLU* 3.4 10.0 + - - +
260A ARG* 3.5 18.7 + - - +
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Residues in contact with LEU 257 (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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117A ASP* 4.6 7.9 - - + +
119A VAL* 4.3 6.5 - - + -
136A THR 4.1 2.0 - - - +
137A SER* 3.7 30.5 - - - +
140A LEU* 3.6 31.2 - - + +
142A ALA* 4.2 12.1 - - + -
215A LEU* 3.6 24.0 - - + -
253A LEU* 2.9 38.2 + - + +
256A ALA* 1.3 71.4 - - - +
258A HIS* 1.3 60.2 + - - +
260A ARG* 2.8 20.2 + - - +
261A ILE* 2.9 13.9 + - - +
264A ASN* 3.7 21.2 - - - +
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Residues in contact with HIS 258 (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 LEU* 4.0 7.7 - - + +
254A GLY 2.8 20.8 + - - +
255A ILE* 3.3 6.7 + - - +
257A LEU* 1.3 76.5 - - - +
259A GLU* 1.3 72.7 + - - +
261A ILE* 3.3 31.8 - - + +
203B VAL* 3.7 20.2 - - + -
204B LYS* 3.6 14.1 + - + -
238B ILE* 4.2 10.7 - - + +
239B PRO* 4.7 10.1 + - + +
255B ILE* 3.5 37.7 - - + +
258B HIS* 4.4 7.2 - + - -
259B GLU* 2.7 29.2 + - - -
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Residues in contact with GLU 259 (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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203A VAL* 3.6 28.7 - - + +
204A LYS* 3.1 46.4 + - - +
206A LEU* 4.7 4.0 - - + -
207A GLY* 3.5 22.2 + - - +
255A ILE 3.1 13.7 + - - +
256A ALA 3.7 8.3 - - - +
257A LEU 3.1 0.2 - - - -
258A HIS* 1.3 78.9 - - + +
260A ARG* 1.3 59.6 + - - +
261A ILE* 3.4 1.3 + - - -
262A ASP* 5.2 1.9 + - - +
204B LYS* 3.3 17.7 + - - +
258B HIS* 2.9 28.8 + - - +
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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