Contacts of the helix formed by residues 86 - 94 (chain A) in PDB entry 1CQE
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ARG* 5.5 9.0 - - - +
84A PRO 3.8 2.2 - - - +
85A SER* 1.3 89.3 - - - +
87A SER* 1.3 57.2 + - - +
89A ILE* 3.5 8.4 + - + +
90A HIS* 2.9 30.8 + - - +
471A GLY 5.4 3.8 - - - +
472A MET* 4.4 11.7 - - + -
513A HIS* 4.7 3.4 + - + +
520A GLU* 3.4 34.1 - - + +
524A GLU* 3.9 32.2 - - + +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.8 11.7 + - - -
86A PRO* 1.3 74.5 - - - +
88A PHE* 1.3 64.7 + - - +
90A HIS* 3.3 3.5 + - - +
91A PHE* 3.1 22.0 + - - +
513A HIS* 4.2 19.3 + - - -
520A GLU* 3.2 18.6 + - - -
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO* 3.4 26.2 - - + -
85A SER* 2.9 27.1 + - - +
87A SER* 1.3 76.0 - - - +
89A ILE* 1.3 66.4 + - + +
91A PHE* 3.2 20.1 - + + +
92A LEU* 3.1 61.8 - - + +
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Residues in contact with ILE 89 (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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84A PRO* 3.2 37.7 - - + +
85A SER 2.9 15.2 + - - +
86A PRO* 3.7 7.6 - - + +
88A PHE* 1.3 80.8 - - + +
90A HIS* 1.3 63.8 + - - +
91A PHE 3.0 1.2 + - - -
92A LEU* 3.1 14.8 + - + +
93A LEU* 3.0 40.4 + - + +
1702A BOG 4.5 34.8 - - + +
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Residues in contact with HIS 90 (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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86A PRO 2.9 19.1 + - - +
87A SER 3.5 5.2 - - - +
88A PHE 3.3 0.2 - - - -
89A ILE* 1.3 76.0 - - - +
91A PHE* 1.3 62.8 + - - +
93A LEU* 3.5 8.3 + - - +
94A THR* 3.0 46.3 + - + +
192A GLN* 6.0 0.4 - - - -
353A SER 4.3 13.0 - - - -
355A TYR* 4.3 9.8 + + - -
513A HIS* 3.4 45.7 + + + +
514A PRO* 5.3 4.5 + - + -
516A SER* 3.5 22.5 + - - -
523A ILE* 3.9 17.8 - - + +
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Residues in contact with PHE 91 (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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87A SER 3.1 12.0 + - - +
88A PHE* 3.2 18.4 - + + +
90A HIS* 1.3 77.0 - - - +
92A LEU* 1.3 85.7 + - + +
94A THR* 3.1 19.1 + - - -
95A HIS* 3.0 54.6 + + + -
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Residues in contact with LEU 92 (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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88A PHE* 3.1 60.8 - - + +
89A ILE* 3.1 13.0 + - + +
91A PHE* 1.3 95.0 - - + +
93A LEU* 1.3 51.7 + - - +
95A HIS* 3.2 12.1 - - - +
100A TRP* 2.7 31.8 + - + -
1702A BOG 4.4 23.8 - - + -
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Residues in contact with LEU 93 (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 ILE* 3.0 39.0 + - + +
90A HIS* 3.9 6.5 - - - +
92A LEU* 1.3 76.1 - - - +
94A THR* 1.3 56.6 + - - +
95A HIS 3.5 0.7 - - - -
100A TRP* 3.5 29.1 + - + +
116A VAL* 6.3 0.9 - - + -
355A TYR* 3.5 43.7 - - + +
356A PHE* 2.7 37.2 + - - +
357A LEU* 4.0 22.8 + - + -
1650A FLP 5.6 0.2 - - - +
1702A BOG 4.4 21.8 - - + -
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Residues in contact with THR 94 (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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90A HIS* 3.0 43.2 + - + +
91A PHE* 3.1 8.2 + - - -
93A LEU* 1.3 79.0 - - - +
95A HIS* 1.3 81.7 + - - +
353A SER 4.5 0.7 - - - +
354A GLY 3.7 24.9 - - - +
355A TYR* 4.4 5.2 - - + -
356A PHE* 3.0 22.7 - - - -
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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