Contacts of the helix formed by residues 65 - 75 (chain A) in PDB entry 2D2C
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 ALA 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.8 18.2 - - - +
59A LYS 3.1 20.4 + - - +
61A THR 3.3 17.4 + - - +
64A GLU* 1.3 75.7 - - - +
66A TYR* 1.3 60.2 + - - +
68A SER* 2.3 28.0 + - - -
69A VAL* 2.7 20.1 + - - +
138A LEU 4.4 0.9 - - - +
139A PRO 4.6 0.2 - - - -
140A TRP* 4.2 19.7 - - + -
180A LEU* 5.6 1.8 - - + -
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Residues in contact with TYR 66 (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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64A GLU 2.6 5.9 + - - -
65A ALA* 1.3 75.3 - - - +
67A ALA* 1.3 60.5 - - + +
68A SER 2.8 5.7 + - - -
69A VAL* 2.9 15.8 + - + +
70A GLN* 3.0 48.6 + - + +
139A PRO 3.8 15.7 - - - -
140A TRP* 2.8 28.5 - + + +
141A ASP* 4.8 3.1 - - - -
62B VAL* 3.9 15.5 - - + +
63B GLY 2.4 46.2 + - - -
64B GLU* 4.7 0.5 - - - -
65B PRO* 2.8 22.2 - - + -
66B ALA* 2.9 36.3 - - + +
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Residues in contact with ALA 67 (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 THR 4.9 2.9 - - - +
64A GLU* 3.1 21.0 + - + +
66A TYR* 1.3 82.6 - - + +
68A SER* 1.3 57.9 + - - +
70A GLN* 3.8 26.8 - - - +
71A TYR* 3.9 6.8 + - - +
140A TRP* 4.9 1.3 - - + -
66B ALA 5.8 1.6 - - - +
67B ASN* 6.1 2.5 - - - +
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Residues in contact with SER 68 (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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57A TYR 4.8 1.9 - - - +
58A TYR* 3.9 6.8 - - - -
59A LYS* 3.4 54.8 + - - +
64A GLU* 4.2 2.1 - - - +
65A ALA* 2.3 33.5 + - - -
67A ALA* 1.3 77.8 - - - +
69A VAL* 1.3 57.8 + - - -
70A GLN 3.2 1.6 - - - -
71A TYR* 2.7 29.5 - - - +
72A ILE* 2.8 10.5 - - - +
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Residues in contact with VAL 69 (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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58A TYR* 4.2 8.5 - - + -
65A ALA 2.7 27.2 + - - +
66A TYR* 2.9 6.0 + - + +
68A SER* 1.3 70.3 - - - +
70A GLN* 1.3 68.3 + - - +
71A TYR 2.8 1.8 - - - -
72A ILE* 2.8 26.3 + - + -
73A MET* 3.1 16.0 + - + +
83A ARG* 3.6 34.1 - - - +
139A PRO* 4.2 15.5 - - + +
301A HEM 3.7 22.7 - - - +
62B VAL* 4.4 11.0 - - + -
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Residues in contact with GLN 70 (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* 3.0 50.8 + - + +
67A ALA* 3.8 21.3 - - - +
69A VAL* 1.3 77.1 - - - +
71A TYR* 1.3 50.1 + - - +
73A MET* 4.8 0.9 - - - -
74A ASN* 2.6 60.1 + - - +
62B VAL* 4.2 24.9 - - + +
66B ALA* 6.0 0.2 - - - +
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Residues in contact with TYR 71 (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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59A LYS* 3.9 24.2 - - - +
67A ALA 3.9 4.8 + - - +
68A SER* 2.7 22.2 + - - +
70A GLN* 1.3 81.6 - - - +
72A ILE* 1.3 61.3 + - + +
74A ASN* 3.9 5.4 - - - -
75A GLU* 3.3 43.6 + - + -
76A VAL* 3.3 15.1 - - + +
45D PRO* 5.3 10.0 - - + +
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Residues in contact with ILE 72 (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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54A MET* 5.8 9.9 - - + -
57A TYR* 4.2 35.4 - - + +
58A TYR* 5.1 5.2 - - + +
68A SER* 2.8 32.1 - - - +
69A VAL* 2.8 31.1 + - + +
71A TYR* 1.3 71.0 - - + +
73A MET* 1.3 61.0 + - + +
75A GLU 2.7 24.4 - - - +
76A VAL* 3.7 9.1 - - + +
79A GLY* 3.2 32.4 - - - +
83A ARG* 4.8 11.7 - - + +
41D TYR* 4.5 12.3 - - + +
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Residues in contact with MET 73 (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 VAL* 3.1 17.6 + - + +
70A GLN* 4.0 2.5 - - - +
72A ILE* 1.3 86.6 - - - +
74A ASN* 1.3 70.3 + - - +
75A GLU 3.0 4.9 + - - +
80A TRP* 3.7 48.1 - - + +
83A ARG* 3.9 26.7 - - + +
84A SER* 4.8 0.7 - - - +
59B PRO* 5.5 1.6 - - + -
60B ALA* 3.0 39.0 - - + +
61B MET* 4.0 9.6 - - + -
62B VAL* 4.1 20.9 - - + -
145C GLY* 5.7 5.4 - - - -
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Residues in contact with ASN 74 (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 GLN* 2.6 44.3 + - - +
71A TYR* 3.7 1.5 + - - +
73A MET* 1.3 74.9 - - - +
75A GLU* 1.3 82.1 + - - +
143C HIS* 4.3 41.7 + - + +
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Residues in contact with GLU 75 (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 TYR* 3.3 37.7 + - + -
72A ILE 2.7 19.9 - - - +
73A MET 3.0 5.1 + - - +
74A ASN* 1.3 109.2 - - - +
76A VAL* 1.3 80.9 + - - +
79A GLY 3.8 1.0 + - - -
80A TRP* 5.0 1.6 - - - -
45D PRO* 4.6 13.7 - - + -
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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