Contacts of the helix formed by residues 119 - 126 (chain A) in PDB entry 2EYQ
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 PRO 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A CYS* 1.3 91.3 - - + +
120A HIS* 1.3 59.8 + - - +
121A SER* 2.9 25.5 + - - +
122A PHE* 3.0 19.2 + - - +
123A LEU 3.9 1.6 + - - -
265A PHE* 3.7 33.2 - - + -
267A GLU* 4.7 13.0 - - + +
268A PRO 4.1 9.4 - - - +
269A LEU* 4.3 5.2 - - + -
270A PRO* 3.8 24.5 - - + -
275A TYR* 3.4 1.6 + - - -
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Residues in contact with HIS 120 (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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95A LEU 4.2 2.0 - - - -
96A TYR* 4.0 24.5 + + - -
99A PRO* 3.8 31.4 - - + +
119A PRO* 1.3 69.2 - - - +
121A SER* 1.3 63.4 + - - +
123A LEU* 4.3 14.1 - - + +
124A HIS* 3.3 38.6 + + + +
270A PRO* 4.9 1.0 - - - +
274A SER 6.0 1.8 - - - +
275A TYR* 3.3 36.1 + + + +
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PRO* 2.9 13.6 + - - +
120A HIS* 1.3 78.9 - - - +
122A PHE* 1.3 75.6 + - - +
124A HIS* 3.9 2.2 - - - +
125A GLY* 2.9 23.2 + - - -
126A HIS* 5.3 0.2 - - - -
265A PHE* 5.6 2.4 - - - -
267A GLU* 5.5 3.6 + - - -
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Residues in contact with PHE 122 (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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118A CYS* 4.2 13.5 - - + -
119A PRO* 3.0 13.2 + - + +
121A SER* 1.3 83.4 + - - +
123A LEU* 1.3 78.9 + - + +
126A HIS* 3.0 52.8 + + - +
213A PRO* 4.0 22.2 - - + -
215A HIS 3.5 14.6 - - - -
216A GLU* 4.0 3.1 - - - -
217A PHE 3.3 28.3 - - - -
218A PRO* 3.1 35.9 - - + -
265A PHE* 3.7 29.6 - + + -
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Residues in contact with LEU 123 (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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92A LEU* 3.8 27.1 - - + +
95A LEU* 3.6 22.4 - - + -
96A TYR* 3.3 48.4 - - + +
118A CYS* 4.5 6.1 - - - -
119A PRO 3.9 2.6 + - - +
120A HIS* 4.1 9.2 + - - +
121A SER 3.5 0.2 - - - -
122A PHE* 1.3 95.0 - - + +
124A HIS* 1.3 65.6 + - - +
125A GLY 3.1 1.6 + - - -
126A HIS 3.8 0.7 - - - -
127A ALA* 3.2 23.7 + - - +
212A LEU* 4.8 7.6 - - + -
213A PRO* 4.0 19.3 - - + +
275A TYR* 4.6 7.0 - - + +
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Residues in contact with HIS 124 (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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96A TYR* 4.5 18.1 + + - -
120A HIS* 3.3 37.1 + + + +
121A SER* 3.4 3.2 + - - +
123A LEU* 1.3 78.7 - - - +
125A GLY* 1.3 61.3 + - - +
127A ALA* 3.9 10.4 - - - +
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Residues in contact with GLY 125 (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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121A SER 2.9 16.7 + - - -
122A PHE 3.9 0.2 - - - -
124A HIS* 1.3 76.1 - - - +
126A HIS* 1.3 61.0 + - - +
127A ALA 3.0 17.2 + - - +
128A LEU* 5.4 1.6 - - - +
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Residues in contact with HIS 126 (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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121A SER 5.3 0.2 - - - -
122A PHE* 3.0 52.3 + + - +
123A LEU 3.8 1.3 - - - -
125A GLY* 1.3 75.3 - - - +
127A ALA* 1.3 59.7 + - - +
128A LEU* 4.5 7.8 - - - +
148A ALA* 6.0 2.6 - - - +
211A LEU* 3.8 10.0 - - - +
213A PRO* 3.7 29.0 - - + +
218A PRO* 4.5 12.4 - - + +
220A ASP* 3.9 21.8 - - - -
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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