Contacts of the helix formed by residues 62 - 70 (chain A) in PDB entry 2WWB
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 PHE 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP* 3.1 32.2 - - + -
61A PRO* 1.4 87.1 - - - +
63A TYR* 1.4 60.6 + - - +
64A TRP 3.6 1.3 - - - -
65A MET* 3.4 13.1 + - - -
66A ARG* 3.1 36.4 + - - +
136A MET* 3.4 27.6 - - + -
302A TYR* 4.5 5.2 - - + -
303A VAL* 5.1 0.4 - - + -
306A GLN* 3.8 14.8 - - - -
334A ARG* 3.5 42.4 - - + +
335A ALA* 3.4 42.6 - - + -
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Residues in contact with TYR 63 (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 ASP* 5.4 4.3 + - - -
62A PHE* 1.4 71.0 - - - +
64A TRP* 1.4 66.0 + - - +
66A ARG* 3.4 49.8 - - - +
67A VAL* 3.9 6.6 - - - +
194A LYS* 6.3 1.6 - - - -
333A ALA* 5.2 7.2 - - + -
334A ARG* 3.4 34.5 - - + +
349A GLU* 5.5 0.7 - - - -
351A PHE* 5.4 10.1 - + + -
442A GLY* 3.5 16.5 - - - +
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Residues in contact with TRP 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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63A TYR* 1.4 79.1 - - - +
65A MET* 1.4 63.9 + - - +
66A ARG 3.5 0.5 + - - -
67A VAL 3.8 3.3 + - - -
68A ILE* 3.1 42.2 - - + +
295A SER* 3.7 29.6 - - - -
298A VAL* 3.5 27.8 - - + -
299A SER* 3.8 6.7 - - - -
302A TYR* 3.6 18.8 - + - +
334A ARG* 3.2 21.9 - - - +
345A LEU 4.9 0.7 - - - -
347A PRO* 3.6 31.6 - - + -
351A PHE* 6.0 1.3 - - + -
364A TYR* 3.8 11.0 + - - -
368A MET* 4.8 8.3 - - + -
436A ASP* 3.6 16.9 + - - -
442A GLY 3.5 10.3 + - - +
443A SER* 3.1 29.7 + - - +
445A THR* 4.2 21.8 + - + -
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Residues in contact with MET 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 PRO* 3.4 24.9 - - + +
62A PHE* 3.7 17.3 - - + +
63A TYR 3.4 0.2 - - - -
64A TRP* 1.4 81.1 - - - +
66A ARG* 1.4 63.0 + - - +
67A VAL 3.4 0.7 + - - -
68A ILE 3.6 1.0 + - - -
69A LEU* 3.5 41.9 + - + +
79A LEU* 5.8 2.5 - - + -
127A GLN* 6.2 2.5 - - - +
131A TYR* 6.0 1.3 - - + -
136A MET* 4.4 7.9 - - + -
299A SER* 3.4 46.1 + - - +
300A ASN* 5.5 1.8 - - - +
302A TYR* 4.0 8.3 - - + -
303A VAL* 3.6 24.7 - - + -
334A ARG* 3.5 12.7 - - - +
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Residues in contact with ARG 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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57A ASP* 3.8 32.1 + - - -
60A ASP* 4.5 8.3 + - - +
61A PRO* 3.8 23.3 - - + +
62A PHE* 3.1 40.9 + - - +
63A TYR* 3.4 50.2 - - - +
64A TRP 3.4 0.2 - - - -
65A MET* 1.4 77.7 - - - +
67A VAL* 1.4 70.4 + - + +
69A LEU* 3.6 2.1 + - - -
70A ALA* 3.4 14.9 + - - -
73A ARG* 3.4 41.5 + - + +
74A GLY* 6.1 0.9 - - - -
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Residues in contact with VAL 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 TYR 3.9 16.6 - - - +
64A TRP 3.8 6.5 + - - +
65A MET 3.4 1.2 - - - -
66A ARG* 1.4 80.9 - - + +
68A ILE* 1.4 64.2 + - + +
70A ALA* 3.3 23.0 + - - +
73A ARG* 5.7 0.2 - - - -
186A ASN* 3.6 12.8 + - - +
187A ILE* 4.1 33.0 - - + +
190A THR* 4.9 18.4 - - + +
441A ILE* 5.3 9.0 - - + +
442A GLY* 4.7 10.1 - - - +
443A SER* 4.4 11.0 - - - +
446A GLY* 5.3 2.7 - - - -
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Residues in contact with ILE 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 TRP* 3.1 60.8 - - + +
65A MET 3.6 1.1 + - - -
66A ARG 3.4 0.6 - - - -
67A VAL* 1.4 77.7 - - + +
69A LEU* 1.4 63.3 + - - +
70A ALA* 4.8 1.6 - - - -
85A VAL* 4.5 7.8 - - - +
183A ILE* 4.5 18.9 - - + +
187A ILE* 5.4 3.1 - - + -
292A ILE* 5.2 4.0 - - + +
295A SER* 3.9 25.1 - - - -
296A ALA* 4.9 8.0 - - - +
299A SER* 4.2 10.0 + - - +
443A SER* 3.7 17.3 - - - +
445A THR* 5.6 1.1 - - + -
446A GLY* 4.7 13.5 - - - +
449A LEU* 3.9 19.5 - - + -
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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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61A PRO* 5.8 1.1 - - + +
65A MET* 3.5 43.2 + - + +
66A ARG* 3.9 4.0 - - - +
67A VAL 3.4 0.4 - - - -
68A ILE* 1.4 77.5 - - - +
70A ALA* 1.4 69.8 + - - +
73A ARG* 3.5 21.3 - - - +
79A LEU* 4.2 9.4 - - + -
82A SER* 3.6 32.9 - - - +
85A VAL* 3.9 16.3 - - + +
86A THR* 4.7 8.7 - - - +
127A GLN* 6.0 4.0 - - - +
182A PHE* 3.5 11.6 - - - -
183A ILE* 3.6 6.8 - - - +
296A ALA* 5.7 2.0 - - + +
299A SER* 4.4 15.7 - - - -
300A ASN* 4.9 8.3 - - - +
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Residues in contact with ALA 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 ARG 3.4 4.7 + - - -
67A VAL 3.3 18.7 + - - +
69A LEU* 1.4 88.5 - - - +
71A SER* 1.4 67.2 + - - +
72A ASN 4.9 0.2 - - - +
73A ARG* 4.6 0.7 - - - -
82A SER 3.5 6.4 + - - -
182A PHE* 3.4 19.9 - - + +
183A ILE* 3.9 31.4 - - + +
186A ASN* 3.6 19.1 - - + +
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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