Contacts of the helix formed by residues 59 - 74 (chain B) in PDB entry 2H3W
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 SER 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B VAL* 1.3 76.2 - - - +
60B GLU* 1.3 65.3 + - - +
61B GLU* 3.6 15.6 + - - +
62B GLU* 2.9 44.4 + - - +
63B TRP* 3.0 21.0 + - - +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER* 1.3 72.6 - - - +
61B GLU* 1.3 72.2 + - - +
63B TRP* 3.5 6.7 + - - +
64B ALA* 3.0 29.6 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.6 19.3 + - - +
60B GLU* 1.3 91.9 + - - +
62B GLU* 1.3 66.2 + - + +
64B ALA* 3.5 6.2 + - - +
65B HIS* 3.1 23.7 + - - +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 3.6 10.9 - - + +
59B SER* 2.9 42.2 + - - +
61B GLU* 1.3 78.0 - - + +
63B TRP* 1.3 56.9 + - - +
65B HIS* 3.6 6.1 + - - +
66B THR* 2.8 33.3 + - - -
540B ASP* 5.1 1.0 - - - +
541B THR* 4.0 20.3 - - + +
542B SER* 3.3 13.6 + - - +
545B ILE* 3.8 16.8 - - - +
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Residues in contact with TRP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 2.8 50.0 + - + +
54B LEU* 4.0 11.4 - - + -
55B GLN* 3.2 44.4 - - + +
58B VAL* 3.8 8.7 - - + +
59B SER 3.0 17.9 + - - +
60B GLU* 3.8 7.0 - - - +
61B GLU 3.2 0.2 - - - -
62B GLU* 1.3 74.5 - - - +
64B ALA* 1.3 64.5 + - + +
66B THR* 3.1 5.8 + - - -
67B LYS* 2.7 64.2 + - + +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU 3.0 18.8 + - - +
61B GLU* 3.8 6.7 - - - +
63B TRP* 1.3 89.0 - - + +
65B HIS* 1.3 62.4 + - - +
67B LYS* 3.2 6.9 + - - +
68B GLN* 3.1 19.8 + - - +
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLU 3.1 18.1 + - - +
62B GLU* 3.7 6.6 + - - +
64B ALA* 1.3 76.5 - - - +
66B THR* 1.3 58.6 + - - +
68B GLN* 2.8 35.5 + - + +
69B LEU* 3.0 44.7 + - + +
540B ASP* 3.9 15.2 + - - -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 4.0 11.9 - - + -
51B LEU* 3.9 9.6 - - + -
54B LEU* 3.6 28.0 - - + -
62B GLU 2.8 14.9 + - - -
63B TRP* 3.5 6.7 - - - -
65B HIS* 1.3 75.6 - - - +
67B LYS* 1.3 56.6 + - - +
69B LEU* 3.2 6.3 + - + +
70B VAL* 2.9 29.8 + - + +
537B ILE* 5.6 2.0 - - + -
540B ASP* 2.5 30.6 + - - +
542B SER* 2.5 21.0 + - - -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.6 35.1 - - + +
63B TRP* 2.7 46.2 + - + +
64B ALA* 3.2 11.4 - - - +
65B HIS 3.1 0.2 - - - -
66B THR* 1.3 72.6 - - - +
68B GLN* 1.3 62.2 + - - +
70B VAL* 3.3 2.4 + - - +
71B ASP* 3.1 47.7 + - - +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA 3.1 9.9 + - - +
65B HIS* 2.8 23.0 + - + +
67B LYS* 1.3 75.6 - - - +
69B LEU* 1.3 66.0 + - + +
71B ASP* 3.3 10.0 + - + +
72B GLU* 3.0 23.6 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 3.0 49.2 + - + +
66B THR* 3.6 6.7 - - - +
68B GLN* 1.3 77.0 - - + +
70B VAL* 1.3 58.7 + - - +
72B GLU* 3.4 8.7 + - + +
73B PHE* 2.8 30.6 + - - +
536B ASP* 4.0 31.9 - - + +
537B ILE* 4.4 13.1 - - + +
540B ASP* 3.7 33.4 - - + +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.9 21.3 - - + +
50B TYR* 4.5 6.7 - - + -
51B LEU* 3.8 35.7 - - + -
66B THR* 2.9 27.3 + - + +
67B LYS* 3.6 5.8 - - - +
68B GLN 3.2 0.2 - - - -
69B LEU* 1.3 73.4 - - - +
71B ASP* 1.3 69.2 + - - +
73B PHE* 3.2 16.0 + - - +
74B GLN* 3.2 35.1 + - - +
537B ILE* 4.1 19.3 - - + -
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Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 3.1 45.7 + - - +
68B GLN* 3.3 11.0 + - + +
70B VAL* 1.3 77.3 - - - +
72B GLU* 1.3 61.1 + - - +
74B GLN* 3.6 12.1 + - - +
75B THR* 3.2 23.9 + - - -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLN 3.0 17.5 + - - +
69B LEU* 3.8 10.1 - - + +
71B ASP* 1.3 76.7 - - - +
73B PHE* 1.3 65.0 - - - +
75B THR* 3.2 39.2 - - - +
78B GLY* 4.7 3.6 - - - -
79B VAL 5.1 0.5 + - - -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.1 14.4 - - + -
47B LEU* 3.9 20.4 - - + -
69B LEU 2.8 18.6 + - - +
70B VAL* 3.2 8.5 + - - +
72B GLU* 1.3 78.1 - - - +
74B GLN* 1.3 58.0 + - - +
75B THR 3.8 0.3 + - - -
78B GLY 4.4 0.3 - - - -
79B VAL* 3.9 11.7 + - + +
80B GLY* 2.8 58.6 + - - -
81B GLU 3.9 1.0 + - - -
83B LEU* 3.9 15.9 - - + -
520B LEU* 5.6 0.2 - - + -
523B LEU* 4.2 12.6 - - + -
535B PRO* 3.9 17.3 - - + -
536B ASP 6.0 0.2 - - - -
537B ILE* 3.8 42.0 - - + -
538B PHE* 4.3 8.7 - + - -
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.7 23.7 - - + +
44B GLN* 3.3 51.2 + - - +
47B LEU* 3.4 15.8 - - + +
70B VAL* 3.2 31.6 + - - +
71B ASP* 3.9 10.9 - - - +
73B PHE* 1.3 75.2 - - - +
75B THR* 1.3 67.4 + - - +
76B SER 3.8 0.5 + - - -
81B GLU* 4.9 6.3 - - - +
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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