Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 1GEY
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO* 4.6 3.8 - - - -
244A PRO 4.4 0.2 + - - -
245A LEU* 1.3 78.6 - - - +
247A THR* 1.3 64.2 + - - +
248A PRO* 3.3 16.9 - - - +
249A VAL* 3.2 25.1 + - - +
250A ALA* 3.1 21.9 + - - +
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Residues in contact with THR 247 (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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49A GLN* 4.5 23.2 - - + +
51A THR* 3.7 23.4 + - - +
52A LEU* 4.2 18.8 - - + -
54A ARG 4.4 6.2 + - - -
56A PRO* 3.2 31.9 - - - +
245A LEU 3.9 0.8 + - - -
246A SER* 1.3 71.4 - - - +
248A PRO* 1.3 69.2 - - + +
250A ALA* 3.9 6.5 - - - +
251A ASP* 3.0 21.9 + - + +
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Residues in contact with PRO 248 (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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47A LEU* 3.8 29.1 - - + +
52A LEU* 3.8 24.7 - - + -
246A SER* 3.3 16.4 - - - +
247A THR* 1.3 94.6 - - + +
249A VAL* 1.3 56.5 + - + +
251A ASP* 3.4 2.5 - - + +
252A ILE* 3.2 37.0 + - + +
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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
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220A GLY 5.7 0.2 - - - +
221A LEU* 3.4 51.5 - - + +
222A ARG 4.8 0.2 - - - +
223A CYS* 4.1 10.3 - - + -
245A LEU* 3.8 26.2 - - + -
246A SER* 3.2 22.9 + - - +
248A PRO* 1.3 78.4 - - + +
250A ALA* 1.3 59.8 + - - +
251A ASP 3.2 0.2 - - - -
252A ILE 3.7 0.2 + - - -
253A ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 250 (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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49A GLN* 5.3 2.4 - - - +
56A PRO* 6.2 0.9 - - + -
60A PRO* 3.6 36.6 - - + -
63A VAL* 3.4 16.6 - - - +
245A LEU* 4.1 7.2 - - + +
246A SER 3.1 15.3 + - - +
247A THR* 3.9 7.9 - - - +
248A PRO 3.4 0.2 - - - -
249A VAL* 1.3 73.6 - - - +
251A ASP* 1.3 64.5 + - - +
253A ALA* 4.3 0.2 - - - -
254A ALA* 3.3 20.6 + - - +
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Residues in contact with ASP 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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47A LEU* 3.6 10.6 - - + +
48A THR* 2.7 37.0 + - - -
49A GLN* 3.0 35.0 + - + +
247A THR 3.0 18.1 + - - +
248A PRO* 3.4 8.3 - - + +
249A VAL 3.2 0.2 - - - -
250A ALA* 1.3 79.2 - - - +
252A ILE* 1.3 62.1 + - - +
254A ALA* 3.4 4.2 + - - +
255A GLN* 2.7 48.3 + - - +
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Residues in contact with ILE 252 (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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45A PHE* 3.6 46.0 - - + +
46A GLN 4.9 1.8 - - - +
47A LEU* 4.2 19.7 - - + -
218A LEU* 4.4 6.3 - - + -
221A LEU* 3.9 35.9 - - + -
248A PRO* 3.2 19.3 + - + +
251A ASP* 1.3 72.8 - - - +
253A ALA* 1.3 59.8 + - - +
255A GLN* 3.2 14.5 + - - +
256A ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 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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63A VAL* 4.2 15.0 - - + -
212A LEU* 4.1 20.9 - - + -
221A LEU* 4.0 6.5 - - + +
223A CYS* 4.1 13.5 - - - -
249A VAL 3.0 21.1 + - - +
250A ALA* 3.9 5.4 - - - +
251A ASP 3.3 0.2 - - - -
252A ILE* 1.3 77.4 - - - +
254A ALA* 1.3 57.7 + - - +
256A ALA* 3.5 2.6 + - - +
257A LEU* 3.0 36.6 + - + +
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Residues in contact with ALA 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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62A ALA* 4.0 27.6 - - + -
63A VAL* 4.4 6.5 - - + +
66A ASN* 3.2 27.3 + - - +
250A ALA 3.3 16.6 + - - +
251A ASP* 3.9 4.9 - - - +
252A ILE 3.3 0.2 - - - -
253A ALA* 1.3 77.0 - - - +
255A GLN* 1.3 64.8 + - + +
257A LEU* 3.5 1.5 + - - -
258A SER* 3.4 12.0 + - - -
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Residues in contact with GLN 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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45A PHE* 4.0 22.9 - - + -
46A GLN 3.1 28.9 + - - +
48A THR* 3.6 16.3 - - + +
251A ASP* 2.7 38.6 + - - +
252A ILE* 3.2 12.3 + - - +
254A ALA* 1.3 79.3 - - + +
256A ALA* 1.3 57.3 + - - +
258A SER* 2.8 26.8 + - - -
261A GLY* 4.3 3.5 - - - -
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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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45A PHE* 3.9 18.8 - - + -
212A LEU* 5.3 0.7 - - + -
216A PHE* 3.8 17.0 - - + -
218A LEU* 3.6 30.3 - - + -
252A ILE 3.0 15.6 + - - +
253A ALA* 3.8 5.8 - - - +
255A GLN* 1.3 77.3 - - - +
257A LEU* 1.3 58.2 + - + +
258A SER 3.4 1.3 - - - -
261A GLY* 3.5 26.9 - - - +
268A ARG* 5.8 1.7 + - - +
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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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63A VAL* 4.1 12.1 - - + +
66A ASN* 3.6 29.3 - - + +
67A TYR* 3.7 44.9 - - + -
70A TYR* 4.8 7.9 - - + -
212A LEU* 4.2 11.9 - - + -
216A PHE* 3.8 28.3 - - + -
225A PHE* 3.9 16.4 - - + -
253A ALA 3.0 24.6 + - - +
254A ALA 3.5 4.0 + - - +
255A GLN 3.2 0.6 - - - -
256A ALA* 1.3 77.4 - - - +
258A SER* 1.3 62.8 + - - +
259A PRO* 4.6 0.7 - - - +
262A ILE* 3.5 15.8 - - + +
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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