Contacts of the helix formed by residues 76 - 89 (chain A) in PDB entry 2YVE
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 ASP 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASP* 3.0 31.2 + - - +
75A GLU* 1.3 78.6 - - - +
77A PRO* 1.3 68.4 - - - +
78A LEU* 2.9 31.2 + - - +
79A GLU* 2.9 32.7 + - + +
80A ARG* 3.1 13.8 + - - +
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Residues in contact with PRO 77 (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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75A GLU 3.4 8.7 - - - +
76A ASP* 1.3 90.4 - - - +
78A LEU* 1.3 67.9 + - + +
80A ARG* 3.4 31.8 + - - +
81A LEU* 3.0 27.7 + - - +
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Residues in contact with LEU 78 (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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76A ASP* 2.9 19.0 + - - +
77A PRO* 1.3 88.5 - - + +
79A GLU* 1.3 61.7 + - + +
81A LEU* 3.7 11.6 - - + +
82A ARG* 3.0 37.4 + - - +
132A HIS* 5.0 13.5 - - + +
136A VAL* 5.0 12.1 - - + -
173A ILE* 4.0 24.9 - - + +
174A PRO* 4.4 13.5 - - + +
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Residues in contact with GLU 79 (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 THR* 3.8 6.4 - - + +
72A ARG* 3.3 30.9 + - - +
73A ASP* 3.6 21.2 - - + +
76A ASP* 2.9 20.6 + - + +
78A LEU* 1.3 76.0 - - + +
80A ARG* 1.3 66.3 + - - +
82A ARG* 3.2 29.3 + - - +
83A ALA* 3.1 23.7 + - - +
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Residues in contact with ARG 80 (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 THR* 4.2 6.1 - - - -
74A PRO* 2.9 38.7 + - + +
75A GLU* 3.3 21.6 + - - +
76A ASP 3.1 3.4 + - - +
77A PRO* 3.6 34.7 - - - +
78A LEU 3.3 0.2 - - - -
79A GLU* 1.3 77.9 - - - +
81A LEU* 1.3 55.9 + - - +
83A ALA* 3.2 3.5 + - - +
84A VAL* 2.9 34.5 + - - +
119A GLN 3.4 26.6 + - - -
120A TRP* 3.8 36.8 + - + +
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Residues in contact with LEU 81 (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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77A PRO 3.0 18.0 + - - +
78A LEU* 3.7 10.1 - - + +
79A GLU 3.3 0.4 - - - -
80A ARG* 1.3 77.0 - - - +
82A ARG* 1.3 61.6 + - - +
84A VAL* 3.2 7.3 + - + +
85A VAL* 3.0 31.7 + - + +
120A TRP 5.2 2.2 + - - +
122A PRO* 4.9 6.1 - - + -
136A VAL* 4.0 39.0 - - + +
139A VAL* 4.1 22.9 - - + -
140A GLN* 4.2 20.2 - - - +
173A ILE* 3.8 35.7 - - + -
174A PRO* 5.2 0.2 - - + -
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Residues in contact with ARG 82 (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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78A LEU* 3.0 26.2 + - - +
79A GLU* 3.2 28.5 + - - +
80A ARG 3.3 0.2 - - - -
81A LEU* 1.3 75.3 - - - +
83A ALA* 1.3 62.8 + - - +
85A VAL* 3.4 3.1 + - - +
86A VAL* 3.2 27.0 + - - +
170A LEU* 3.8 20.1 + - + +
173A ILE* 3.6 21.3 - - + -
2005A GOL 3.5 30.7 + - - -
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Residues in contact with ALA 83 (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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67A LEU* 4.0 6.1 - - + -
70A ILE* 3.9 22.6 - - + +
71A THR* 3.0 31.9 - - + +
79A GLU 3.1 15.0 + - - +
80A ARG 3.7 3.4 - - - +
82A ARG* 1.3 73.0 - - - +
84A VAL* 1.3 66.7 + - - +
86A VAL* 3.2 6.5 + - - +
87A THR* 2.9 26.5 + - - +
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Residues in contact with VAL 84 (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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63A TRP* 4.6 3.1 - - + -
67A LEU* 3.8 17.5 - - + -
80A ARG 2.9 19.9 + - - +
81A LEU* 3.2 8.0 + - + +
83A ALA* 1.3 76.3 - - - +
85A VAL* 1.3 65.3 + - + +
87A THR* 2.8 23.2 + - - -
88A LEU* 3.0 28.5 + - + +
120A TRP* 3.5 30.3 - - + +
121A ILE* 3.7 25.8 - - + -
140A GLN* 3.9 11.2 - - - +
143A ALA* 5.6 0.2 - - + -
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Residues in contact with VAL 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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81A LEU* 3.0 26.6 + - + +
82A ARG 3.6 4.9 - - - +
83A ALA 3.3 0.2 - - - -
84A VAL* 1.3 76.8 - - + +
86A VAL* 1.3 62.1 + - - +
88A LEU* 3.2 3.5 + - - +
89A ALA* 3.2 21.0 + - - +
139A VAL* 3.6 30.1 - - + -
140A GLN* 5.8 0.4 - - - -
143A ALA* 4.0 22.2 - - + +
146A LEU* 5.7 0.6 - - + +
166A LEU* 3.5 20.9 - - + -
169A ILE* 3.7 24.9 - - + -
170A LEU* 4.0 12.8 - - + -
173A ILE* 4.7 0.4 - - + -
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Residues in contact with VAL 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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66A GLU* 5.4 1.8 - - - +
70A ILE* 4.0 19.7 - - + -
82A ARG 3.2 16.5 + - - +
83A ALA* 3.2 8.5 + - - +
85A VAL* 1.3 74.1 - - - +
87A THR* 1.3 64.4 + - - +
89A ALA* 3.2 15.1 + - - +
90A GLU* 4.4 2.3 + - - +
166A LEU* 3.9 27.5 - - + +
170A LEU* 4.6 10.8 - - + -
1001A MBT 5.2 2.0 - - - -
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Residues in contact with THR 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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63A TRP* 3.0 24.5 + - - -
66A GLU* 3.5 33.2 - - + +
67A LEU* 3.6 16.2 - - + -
70A ILE* 3.9 7.2 - - + -
83A ALA 2.9 18.6 + - - +
84A VAL* 2.8 19.9 + - - -
86A VAL* 1.3 77.1 - - - +
88A LEU* 1.3 59.7 + - - +
89A ALA 3.5 0.5 + - - -
90A GLU* 4.0 9.5 + - - +
1001A MBT 3.4 39.5 - - - -
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Residues in contact with LEU 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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63A TRP* 4.4 3.4 - - + -
84A VAL* 3.0 29.1 + - + +
85A VAL 3.2 4.9 + - - +
87A THR* 1.3 76.0 - - - +
89A ALA* 1.3 63.0 + - - +
90A GLU 3.2 4.4 + - - +
140A GLN* 3.5 28.0 - - - +
143A ALA* 3.8 25.3 - - + +
144A ASP* 3.5 11.7 - - - +
146A LEU* 5.2 0.2 - - - -
147A PHE* 3.2 42.8 + - + -
1001A MBT 3.4 47.6 - - + -
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Residues in contact with ALA 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 VAL 3.2 10.4 + - - +
86A VAL 3.2 13.4 + - - +
88A LEU* 1.3 78.7 - - - +
90A GLU* 1.3 58.1 + - - +
146A LEU* 3.8 24.1 - - + +
162A ARG* 2.8 37.4 + - + +
166A LEU* 4.0 25.8 - - + -
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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