Contacts of the helix formed by residues 59 - 74 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A VAL* 1.3 75.2 - - - +
60A GLU* 1.3 59.8 + - - +
61A GLU* 3.3 17.6 + - - +
62A GLU* 2.8 42.9 + - - +
63A TRP* 2.8 28.7 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL 4.0 0.2 + - - -
59A SER* 1.3 74.7 - - - +
61A GLU* 1.3 71.2 + - - +
63A TRP* 3.4 6.2 + - - +
64A ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.2 17.9 + - - +
60A GLU* 1.3 89.4 + - - +
62A GLU* 1.3 62.4 + - + +
64A ALA* 3.4 6.8 + - - +
65A HIS* 3.1 22.3 + - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.5 10.9 - - + +
59A SER* 2.8 42.3 + - - +
61A GLU* 1.3 74.5 - - + +
63A TRP* 1.3 60.7 + - - +
65A HIS* 3.3 8.0 + - - +
66A THR* 2.9 31.0 + - - -
540A ASP* 5.2 1.0 - - - +
541A THR* 4.0 19.6 - - + +
542A SER* 3.5 15.8 + - - +
545A ILE* 4.0 15.6 - - - +
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Residues in contact with TRP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 2.8 54.0 + - + +
52A LYS* 5.9 0.2 - - - -
54A LEU* 4.0 6.7 - - + -
55A GLN* 3.7 37.7 - - + +
58A VAL* 3.7 14.5 - - + +
59A SER 2.8 17.7 + - - +
60A GLU* 3.8 7.4 - - - +
62A GLU* 1.3 77.6 - - - +
64A ALA* 1.3 64.3 + - + +
66A THR* 3.2 5.8 + - - -
67A LYS* 2.8 56.5 + - + -
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Residues in contact with ALA 64 (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 GLU 2.9 19.0 + - - +
61A GLU* 3.6 7.0 - - - +
62A GLU 3.3 0.2 - - - -
63A TRP* 1.3 86.8 - - + +
65A HIS* 1.3 61.5 + - - +
67A LYS* 3.3 6.6 - - - +
68A GLN* 3.3 26.9 + - - +
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Residues in contact with HIS 65 (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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61A GLU 3.1 13.3 + - - +
62A GLU* 3.6 10.5 - - - +
64A ALA* 1.3 74.9 - - - +
66A THR* 1.3 63.6 + - - +
68A GLN* 3.1 13.9 + - + +
69A LEU* 3.0 51.4 + - + +
540A ASP* 3.8 19.0 + - + -
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Residues in contact with THR 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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50A TYR* 4.0 13.2 - - + -
51A LEU* 3.8 10.8 - - + -
54A LEU* 3.7 26.0 - - + -
62A GLU 2.9 9.4 + - - -
63A TRP* 3.6 7.0 - - - -
65A HIS* 1.3 77.0 - - - +
67A LYS* 1.3 53.7 + - - +
69A LEU* 2.9 5.6 + - - +
70A VAL* 2.8 36.5 + - + +
537A ILE* 5.3 4.5 - - + -
540A ASP* 2.6 21.2 + - - +
542A SER* 2.6 29.2 + - - -
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Residues in contact with LYS 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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51A LEU* 4.0 28.5 - - + +
63A TRP* 2.8 45.2 + - + +
64A ALA* 3.3 8.7 - - - +
66A THR* 1.3 77.1 - - - +
68A GLN* 1.3 68.0 + - - +
70A VAL* 3.5 2.0 + - - +
71A ASP* 3.0 57.2 + - - +
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Residues in contact with GLN 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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64A ALA 3.3 14.7 + - - +
65A HIS* 3.1 14.0 + - + +
67A LYS* 1.3 85.1 - - - +
69A LEU* 1.3 66.5 + - + +
71A ASP* 3.4 15.4 + - - +
72A GLU* 3.2 23.0 + - - +
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Residues in contact with LEU 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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65A HIS* 3.0 44.5 + - + +
66A THR* 2.9 7.6 + - - +
68A GLN* 1.3 78.7 - - + +
70A VAL* 1.3 58.8 + - - +
72A GLU* 3.5 5.7 + - + +
73A PHE* 2.8 32.5 + - - +
536A ASP* 4.1 24.9 - - + +
537A ILE* 4.2 23.0 - - + +
540A ASP* 3.5 35.9 - - + +
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Residues in contact with VAL 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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47A LEU* 3.8 29.8 - - + +
50A TYR* 4.6 6.3 - - + -
51A LEU* 3.8 36.3 - - + -
66A THR* 2.8 24.5 + - + +
67A LYS* 3.6 5.6 - - - +
69A LEU* 1.3 74.7 - - - +
71A ASP* 1.3 68.4 + - - +
73A PHE* 3.2 6.7 + - - +
74A GLN* 3.0 32.2 + - - +
537A ILE* 4.0 19.7 - - + -
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Residues in contact with ASP 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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67A LYS* 3.0 49.4 + - - +
68A GLN* 3.4 15.8 + - - +
70A VAL* 1.3 79.3 - - - +
72A GLU* 1.3 62.4 + - - +
74A GLN* 3.6 17.1 - - - +
75A THR* 3.2 22.7 + - - -
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Residues in contact with GLU 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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68A GLN 3.2 13.8 + - - +
69A LEU* 3.8 6.1 - - + +
71A ASP* 1.3 78.0 - - - +
73A PHE* 1.3 65.0 + - - +
75A THR* 3.1 37.9 - - - +
78A GLY* 4.9 1.9 - - - -
79A VAL 5.2 0.5 + - - -
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Residues in contact with PHE 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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43A LEU* 4.2 6.1 - - + -
47A LEU* 4.0 19.3 - - + -
69A LEU 2.8 21.5 + - - +
70A VAL* 3.5 5.2 - - - +
72A GLU* 1.3 78.7 - - - +
74A GLN* 1.3 58.1 + - - +
75A THR 3.8 0.2 + - - -
78A GLY 4.6 0.2 - - - -
79A VAL* 4.1 12.5 + - + +
80A GLY* 2.9 57.4 + - - -
81A GLU 4.0 0.9 + - - -
83A LEU* 3.9 17.5 - - + -
520A LEU* 6.0 0.2 - - + -
523A LEU* 4.0 25.8 - - + -
535A PRO* 3.9 24.9 - - + -
537A ILE* 4.0 36.3 - - + -
538A PHE* 4.4 5.4 - + - -
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Residues in contact with GLN 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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43A LEU* 4.2 16.1 - - + +
44A GLN* 3.3 54.4 + - - +
47A LEU* 3.1 35.3 - - + +
70A VAL* 3.0 23.4 + - - +
71A ASP* 3.6 19.8 - - - +
73A PHE* 1.3 75.5 - - - +
75A THR* 1.3 66.6 + - - +
76A SER* 3.7 0.7 + - - -
81A GLU* 5.1 3.5 - - - +
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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