Contacts of the helix formed by residues 245 - 257 (chain A) in PDB entry 1EQB
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 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A GLY* 1.3 76.0 - - - -
246A GLU* 1.3 65.8 + - - +
247A GLU* 3.2 10.5 + - - +
248A LEU* 3.2 24.1 + - - +
249A TYR* 3.2 24.8 + - - -
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Residues in contact with GLU 246 (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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245A SER* 1.3 74.3 - - - +
247A GLU* 1.3 56.8 + - - +
249A TYR* 3.5 8.7 + - - +
250A LYS* 3.0 43.5 + - - +
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Residues in contact with GLU 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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245A SER* 3.1 10.2 + - - +
246A GLU* 1.3 80.2 - - - +
248A LEU* 1.3 56.8 + - - +
250A LYS* 3.0 9.7 + - - +
251A LYS* 2.9 41.4 + - - +
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Residues in contact with LEU 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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109A LEU* 3.4 32.8 - - + -
196A TYR* 5.3 7.6 - - + +
221A HIS* 4.2 27.1 - - + +
222A VAL* 4.5 7.4 - - + -
244A GLY* 4.2 19.5 - - - -
245A SER* 3.2 18.5 + - - +
247A GLU* 1.3 78.6 - - - +
249A TYR* 1.3 66.0 + - + +
251A LYS* 3.4 10.4 + - + +
252A LEU* 3.0 39.7 + - + +
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Residues in contact with TYR 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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89A ASP* 2.6 32.0 + - - -
90A TYR* 3.5 43.6 - + + -
241A ALA* 3.6 21.3 - - + -
242A LYS* 3.6 4.5 + - - -
243A GLY 3.5 2.3 + - - -
244A GLY* 2.8 46.0 + - - -
245A SER 3.2 14.1 + - - +
246A GLU* 4.0 7.0 - - - +
248A LEU* 1.3 84.0 - - + +
250A LYS* 1.3 65.8 + - - +
252A LEU* 3.8 5.1 - - + +
253A ASN* 3.0 32.1 + - - +
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Residues in contact with LYS 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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246A GLU* 3.0 27.1 + - - +
247A GLU* 3.2 13.2 - - - +
249A TYR* 1.3 78.3 - - - +
251A LYS* 1.3 64.4 + - + +
253A ASN* 3.1 9.1 + - - +
254A SER* 3.0 29.8 + - - +
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Residues in contact with LYS 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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108A ALA* 3.7 30.4 + - + +
109A LEU* 5.4 4.9 - - + +
196A TYR* 5.6 3.4 + - - -
247A GLU* 2.9 23.9 + - - +
248A LEU* 3.6 12.8 - - + +
250A LYS* 1.3 78.4 - - + +
252A LEU* 1.3 57.0 + - - +
254A SER* 3.1 7.9 + - - -
255A ALA* 2.8 30.5 + - - +
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TYR* 3.4 35.2 + - + +
104A ALA 5.0 0.7 - - - +
105A VAL* 4.4 16.8 - - + +
108A ALA* 4.0 16.6 - - + -
109A LEU* 5.2 2.5 - - + -
222A VAL* 4.0 40.6 - - + -
239A ILE* 4.3 10.6 - - + +
241A ALA* 4.8 2.7 - - + -
248A LEU* 3.0 34.2 + - + +
249A TYR* 3.8 8.3 - - + +
250A LYS 3.2 0.2 - - - -
251A LYS* 1.3 77.0 - - - +
253A ASN* 1.3 61.2 + - - +
255A ALA* 3.4 5.4 + - + +
256A VAL* 3.3 26.2 + - - +
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Residues in contact with ASN 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A TYR* 2.6 48.6 + - + +
90A TYR* 2.7 31.3 + - - -
91A ALA 5.3 0.7 - - - +
92A ASN* 3.0 14.1 + - - +
249A TYR* 3.0 24.0 + - - +
250A LYS* 3.7 6.4 - - - +
252A LEU* 1.3 76.7 - - - +
254A SER* 1.3 57.6 + - - +
257A PHE 3.0 18.5 + - - +
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Residues in contact with SER 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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250A LYS* 3.0 18.7 + - - +
251A LYS* 3.6 10.5 - - - -
253A ASN* 1.3 76.4 - - - +
255A ALA* 1.3 56.1 + - - +
257A PHE 3.2 11.6 - - - -
258A PRO* 3.5 6.4 - - - +
259A GLY* 2.8 33.3 + - - -
133B VAL 5.0 0.3 - - - +
2293B FFO 5.8 0.5 + - - -
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PHE* 5.5 0.5 - - - -
104A ALA* 3.4 38.1 - - + +
107A THR* 4.1 9.6 + - - +
108A ALA* 3.4 22.0 - - + -
251A LYS 2.8 8.5 + - - +
252A LEU* 3.6 5.6 - - - +
254A SER* 1.3 76.7 - - - +
256A VAL* 1.3 53.8 + - - +
259A GLY* 3.3 5.4 - - - -
260A GLY* 2.8 30.7 + - - -
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Residues in contact with VAL 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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59A TYR* 3.6 17.0 - - - +
92A ASN* 3.7 10.3 - - - +
94A GLN* 4.1 18.6 - - + +
95A PRO* 4.1 8.7 - - + -
104A ALA* 3.8 10.8 - - + -
239A ILE* 3.5 31.9 - - + -
252A LEU 3.3 8.8 + - - +
253A ASN 3.8 0.2 - - - +
254A SER 3.2 0.4 - - - -
255A ALA* 1.3 76.9 - - - +
257A PHE* 1.3 61.1 + - + +
260A GLY* 3.4 1.4 + - - -
261A GLN* 2.9 54.3 + - - +
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Residues in contact with PHE 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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57A GLU* 3.5 35.2 - - + -
58A GLY* 3.5 33.2 - - - -
59A TYR* 4.3 15.5 - + + +
64A TYR* 3.9 15.3 - + - -
94A GLN* 4.7 7.6 - - - +
253A ASN 3.0 17.5 + - - +
254A SER* 3.2 10.1 + - - +
256A VAL* 1.3 82.7 - - + +
258A PRO* 1.3 79.4 - - + +
261A GLN* 3.3 22.7 - - + +
262A GLY 3.6 13.5 - - - +
127B LEU* 4.1 7.0 - - + -
2293B FFO 3.5 24.5 - + - -
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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