Contacts of the helix formed by residues 87 - 99 (chain A) in PDB entry 2EUG
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ILE 3.7 1.8 - - - +
86A PRO* 1.3 86.8 - - + +
88A SER* 1.3 62.1 + - - +
90A LEU* 3.3 16.4 + - + +
91A ASN* 3.1 28.1 + - - -
190A PRO* 3.5 31.4 - - + -
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Residues in contact with SER 88 (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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66A TYR* 4.6 7.2 - - - -
77A PHE* 4.1 24.5 - - - -
86A PRO* 3.1 2.2 + - - +
87A PRO* 1.3 77.0 - - - +
89A LEU* 1.3 62.7 + - - +
91A ASN 3.3 1.6 + - - -
92A MET* 3.1 27.0 + - - +
187A HIS* 3.5 8.1 - - - -
188A PRO* 3.7 17.1 - - - +
189A SER* 3.3 27.1 - - - +
190A PRO* 4.4 1.1 - - - +
230A URA 5.2 5.9 + - - -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 4.2 2.2 + - - +
77A PHE 3.5 23.6 - - - +
85A ILE* 3.4 17.7 - - + -
86A PRO* 2.9 12.7 + - + +
88A SER* 1.3 74.5 - - - +
90A LEU* 1.3 56.1 + - - +
92A MET* 3.1 25.6 + - + -
93A TYR* 2.8 61.4 + - + +
109A GLY* 3.4 42.2 - - - +
111A LEU* 4.3 11.4 - - + -
114A TRP* 4.9 1.1 - - + -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.2 50.5 - - + +
86A PRO 3.0 8.2 + - - +
87A PRO* 3.6 18.4 - - + +
89A LEU* 1.3 76.5 - - - +
91A ASN* 1.3 59.5 + - - +
93A TYR* 3.1 7.7 + - - +
94A LYS* 2.9 39.4 + - - +
105A ARG* 3.8 30.0 + - - +
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Residues in contact with ASN 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 PRO* 3.1 14.9 + - - +
88A SER 3.3 1.3 + - - +
89A LEU 3.2 0.2 - - - -
90A LEU* 1.3 71.8 - - - +
92A MET* 1.3 63.8 + - - +
94A LYS* 3.0 30.1 + - - -
95A GLU 3.2 18.0 + - - -
188A PRO* 2.9 32.4 + - + +
190A PRO* 3.7 22.8 - - - +
193A ALA* 3.7 8.8 - - + +
194A HIS* 5.6 1.0 + - - -
197A PHE* 3.4 6.0 - - + -
198A PHE* 3.2 33.8 - - + -
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Residues in contact with MET 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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60A ILE* 5.0 1.1 - - + -
77A PHE* 3.8 37.5 - - + -
88A SER 3.1 16.9 + - - +
89A LEU* 3.3 20.9 - - + +
91A ASN* 1.3 77.4 - - - +
93A TYR* 1.3 61.5 + - + +
95A GLU* 3.4 4.2 + - - +
96A LEU* 3.1 28.1 + - - +
111A LEU* 4.7 0.2 - - + -
114A TRP* 3.7 33.2 - - + -
121A LEU* 5.9 0.4 - - + -
164A TRP* 3.6 37.9 - - + -
188A PRO* 3.9 11.0 - - + -
197A PHE* 3.8 11.7 - - + -
203A PHE* 4.0 6.4 - - + -
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Residues in contact with TYR 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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85A ILE* 3.8 23.3 - - + -
89A LEU* 2.8 39.4 + - + +
90A LEU* 3.1 9.4 + - - +
92A MET* 1.3 73.2 - - - +
94A LYS* 1.3 56.8 + - - +
96A LEU* 3.4 11.0 + - + +
97A GLU* 2.8 30.4 + - - +
103A PHE* 3.7 16.8 - + + -
105A ARG* 4.0 24.1 + - - +
106A PRO* 3.5 29.8 - - + -
108A HIS 2.8 28.4 + - - -
109A GLY* 3.5 10.2 - - - -
111A LEU* 3.8 6.2 - - + +
114A TRP* 4.6 5.4 - + - -
222A PRO* 3.4 24.4 - - + +
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Residues in contact with LYS 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 LEU* 2.9 27.1 + - - +
91A ASN* 3.0 32.3 + - - +
92A MET 3.2 0.6 - - - -
93A TYR* 1.3 78.3 - - - +
95A GLU* 1.3 62.3 + - - +
97A GLU* 3.1 6.1 + - - +
98A ASN* 2.9 35.7 + - - +
105A ARG* 3.9 26.0 - - - +
194A HIS* 5.7 3.4 + - - -
198A PHE* 3.8 16.7 - - + -
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Residues in contact with GLU 95 (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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91A ASN 3.2 2.6 + - - -
92A MET 3.8 3.4 - - - +
94A LYS* 1.3 74.6 - - - +
96A LEU* 1.3 65.2 + - - +
98A ASN* 3.1 8.9 + - - +
99A THR* 2.8 41.1 + - + +
197A PHE* 3.6 32.8 - - + +
198A PHE* 3.4 11.2 - - + +
199A GLY* 2.9 26.2 + - - -
200A CYS* 3.3 3.5 + - - -
201A ASN* 2.6 35.6 + - - +
203A PHE* 4.0 20.6 - - + -
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Residues in contact with LEU 96 (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 MET 3.1 19.5 + - - +
93A TYR* 3.5 13.7 - - + +
95A GLU* 1.3 78.0 - - - +
97A GLU* 1.3 57.5 + - - +
99A THR* 3.7 2.9 - - - -
100A ILE* 2.8 49.9 + - + +
103A PHE* 3.6 32.5 - - + +
114A TRP* 3.9 30.5 - - + -
203A PHE* 3.3 40.2 - - + -
220A TRP* 3.6 14.6 - - + +
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Residues in contact with GLU 97 (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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93A TYR 2.8 20.6 + - - +
94A LYS* 3.1 7.8 + - - +
96A LEU* 1.3 74.1 - - - +
98A ASN* 1.3 69.1 + - - +
99A THR 3.5 0.5 + - - -
100A ILE 4.4 5.9 - - - +
103A PHE* 3.0 35.0 - - + +
104A THR* 3.4 9.1 - - - +
105A ARG* 3.2 34.7 + - - +
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Residues in contact with ASN 98 (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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94A LYS* 2.9 27.1 + - - +
95A GLU* 3.8 10.9 + - - +
96A LEU 3.1 0.4 - - - -
97A GLU* 1.3 88.4 - - - +
99A THR* 1.3 63.3 + - + +
198A PHE* 5.6 3.8 - - - +
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Residues in contact with THR 99 (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 GLU* 2.8 43.6 + - - +
96A LEU* 3.6 5.0 + - - -
97A GLU 3.3 0.4 - - - -
98A ASN* 1.3 85.7 - - + +
100A ILE* 1.3 70.7 + - - +
101A PRO* 3.5 9.5 - - - +
201A ASN* 3.4 31.7 + - + +
203A PHE* 4.7 5.9 - - - +
204A VAL* 3.5 12.6 - - - +
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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