Contacts of the helix formed by residues 84 - 98 (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 HIS 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TRP 4.8 0.4 + - - -
82A SER 3.8 0.4 + - - -
83A PRO* 1.3 74.2 - - - +
85A GLN* 1.3 81.5 + - + +
86A ASP* 2.9 57.4 + - + +
87A ILE* 3.0 33.5 + - + +
88A ILE* 3.3 5.1 + - - +
785A ALA* 3.8 24.9 - - + +
907A HIS* 3.7 9.6 - - - -
908A HIS* 3.5 27.0 + - - -
909A GLN* 3.5 31.1 + - + +
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Residues in contact with GLN 85 (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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83A PRO 3.8 1.8 + - - -
84A HIS* 1.3 84.7 + - + +
86A ASP* 1.3 79.2 + - - +
87A ILE 2.7 1.6 + - - -
88A ILE* 2.6 32.3 + - - +
89A SER* 2.8 14.2 + - - -
151A ARG* 5.6 3.8 - - - +
158A GLU* 3.3 47.6 + - + +
159A HIS* 3.3 36.3 + - + +
172A PHE* 5.5 0.3 - - - -
174A MET* 4.9 7.5 - - + +
463A ARG* 5.8 3.2 - - - +
785A ALA* 5.9 0.6 - - - +
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Residues in contact with ASP 86 (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 HIS* 2.9 28.4 + - + +
85A GLN* 1.3 96.8 + - - +
87A ILE* 1.3 56.6 + - - +
89A SER* 3.9 3.7 + - - -
90A SER* 3.1 26.0 + - - -
159A HIS* 3.7 25.5 + - + -
463A ARG* 5.8 2.6 + - - -
907A HIS* 2.6 47.6 + - + +
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Residues in contact with ILE 87 (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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71A ALA* 4.2 14.1 - - + +
72A ASP 3.5 33.7 - - - +
73A TRP* 3.7 20.2 - - - +
74A GLU* 3.9 22.4 - - + +
83A PRO* 4.7 4.7 - - + -
84A HIS* 3.0 25.5 + - + +
85A GLN 2.7 5.5 + - - -
86A ASP* 1.3 72.8 - - - +
88A ILE* 1.3 62.0 + - - +
90A SER* 3.1 7.0 + - - -
91A ARG* 2.9 38.3 + - + +
907A HIS 4.2 12.1 - - - +
908A HIS* 4.2 11.0 - - + +
909A GLN* 5.4 0.9 - - + +
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Residues in contact with ILE 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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73A TRP* 5.0 0.4 - - - +
83A PRO* 3.6 37.9 - - + +
84A HIS 3.3 4.0 + - - +
85A GLN* 2.6 15.3 + - - +
87A ILE* 1.3 71.3 - - + +
89A SER* 1.3 64.4 + - - +
91A ARG* 3.7 6.6 - - - +
92A LEU* 3.0 35.8 + - + +
174A MET* 4.5 10.5 - - + -
215A HIS* 4.4 23.6 - - + +
216A GLU* 4.1 30.7 - - + +
217A PHE* 6.1 0.4 - - + -
258A GLU* 4.1 19.1 - - + +
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Residues in contact with SER 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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85A GLN 2.8 17.1 + - - -
86A ASP 4.0 2.7 + - - -
88A ILE* 1.3 74.0 - - - +
90A SER* 1.3 66.5 + - - +
92A LEU* 3.4 1.5 + - - +
93A SER* 2.9 23.2 + - - -
159A HIS* 3.5 35.9 + - - -
174A MET* 2.7 39.6 + - - +
175A GLY 4.6 1.4 + - - -
176A SER 3.9 4.0 + - - -
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Residues in contact with SER 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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69A ASN 4.6 10.5 + - - -
71A ALA* 4.5 12.0 - - - +
86A ASP 3.1 17.9 + - - -
87A ILE* 3.3 7.4 - - - -
89A SER* 1.3 81.3 + - - +
91A ARG* 1.3 63.3 + - - +
93A SER* 3.1 9.9 + - - -
94A THR* 2.9 24.4 + - - -
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Residues in contact with ARG 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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70A LEU* 4.0 20.4 - - + +
71A ALA* 3.1 28.1 + - + +
73A TRP* 2.5 52.7 - - - +
87A ILE* 2.9 21.0 + - + +
88A ILE* 3.7 4.0 - - - +
90A SER* 1.3 72.1 - - - +
92A LEU* 1.3 69.7 + - - +
94A THR* 2.6 20.8 + - - +
95A LEU* 2.8 20.3 + - + +
112A THR* 3.9 18.6 + - - +
115A GLN* 3.7 23.5 + - - +
116A ARG 5.6 1.4 + - - -
117A VAL* 4.9 13.0 - - - +
216A GLU* 3.2 32.5 + - - +
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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 ILE* 3.0 21.8 + - + +
89A SER 3.8 3.4 - - - +
91A ARG* 1.3 77.0 - - - +
93A SER* 1.3 63.9 + - - +
95A LEU* 4.7 5.6 - - + +
96A TYR* 3.0 27.2 + - - +
118A CYS* 5.2 3.6 - - - -
122A PHE* 5.0 0.2 - - + -
123A LEU* 3.8 23.6 - - + +
174A MET* 4.0 12.8 - - + -
212A LEU* 3.5 18.8 - - + +
213A PRO* 3.6 25.8 - - + +
215A HIS 3.7 24.9 - - - +
216A GLU* 3.5 29.8 - - + +
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Residues in contact with SER 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 SER 2.9 13.8 + - - -
90A SER* 3.1 12.8 - - - -
91A ARG 2.8 1.2 + - - -
92A LEU* 1.3 78.8 - - - +
94A THR* 1.3 67.4 + - - +
96A TYR* 3.6 3.0 - - - +
97A GLN* 3.1 21.5 + - - +
175A GLY* 4.1 19.0 + - - -
212A LEU* 3.9 9.1 - - - +
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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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68A MET* 4.4 17.2 - - - +
69A ASN 3.8 13.9 + - - -
70A LEU* 3.7 23.6 - - + -
90A SER* 2.9 12.1 + - - -
91A ARG* 2.6 12.1 + - - -
93A SER* 1.3 69.7 + - - +
95A LEU* 1.3 69.6 + - - +
97A GLN* 3.0 9.9 + - - +
98A LEU* 2.8 27.6 + - + +
106A LEU* 3.7 31.2 - - + -
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Residues in contact with LEU 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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70A LEU* 3.8 22.9 - - + -
91A ARG* 2.8 27.4 + - + +
92A LEU* 5.2 2.5 - - + -
94A THR* 1.3 74.9 - - + +
96A TYR* 1.3 64.2 + - - +
97A GLN 3.0 0.5 + - - -
98A LEU* 3.0 13.3 + - + +
99A PRO* 3.3 12.5 - - - +
117A VAL* 3.3 33.4 - - + -
118A CYS* 3.7 17.5 - - - -
120A HIS* 4.2 0.2 - - - -
123A LEU* 3.6 13.2 - - + -
216A GLU* 4.3 14.6 - - - +
272A LEU* 3.9 22.7 - - + -
275A TYR* 3.5 17.1 - - + -
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Residues in contact with TYR 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 LEU 3.0 19.9 + - - +
93A SER* 3.6 4.5 - - - +
95A LEU* 1.3 76.7 - - - +
97A GLN* 1.3 66.0 + - + +
99A PRO* 4.0 1.9 - - - +
100A THR* 5.2 2.8 + - - -
120A HIS* 4.0 14.5 + + - -
123A LEU* 3.3 32.4 - - + +
124A HIS* 4.5 16.2 + - - -
127A ALA* 3.9 28.3 - - + +
210A ASN* 3.8 27.3 + - - -
212A LEU* 3.8 24.0 - - + -
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Residues in contact with GLN 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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68A MET* 3.7 37.0 - - - +
93A SER* 3.1 12.6 + - - +
94A THR* 3.0 7.8 + - - +
96A TYR* 1.3 85.7 - - + +
98A LEU* 1.3 74.2 + - - +
99A PRO 3.5 0.7 - - - -
100A THR* 3.0 23.8 + - - +
101A MET* 3.4 27.4 + - - +
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Residues in contact with LEU 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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41A PRO* 6.0 0.2 - - + -
43A VAL* 5.6 1.3 - - + -
70A LEU* 5.9 0.4 - - + -
94A THR* 2.8 22.6 + - + +
95A LEU* 3.0 11.9 + - - +
97A GLN* 1.3 78.6 + - - +
99A PRO* 1.3 61.1 - - + +
101A MET* 2.7 54.6 + - + +
106A LEU* 4.1 22.7 - - + -
272A LEU* 4.6 10.5 - - + -
275A TYR* 3.5 31.0 - - + +
276A PHE* 4.1 19.5 - - + -
277A PRO* 3.2 14.3 - - + +
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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