Contacts of the helix formed by residues 68 - 79 (chain A) in PDB entry 2PWA
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 GLY 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ASP* 2.9 20.7 + - - -
67A ASN* 1.3 73.9 - - - +
69A HIS* 1.3 64.3 + - - +
70A GLY 3.3 2.2 - - - -
71A THR* 3.1 3.3 + - - -
72A HIS 2.9 19.9 + - - -
212A TRP* 3.5 26.7 - - - -
213A ILE* 3.8 14.0 - - - +
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Residues in contact with HIS 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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39A ASP* 2.7 29.6 + - - +
40A THR* 3.8 7.9 + - + +
67A ASN* 3.0 18.5 + - - +
68A GLY* 1.3 75.7 - - - +
70A GLY* 1.3 57.5 + - - +
72A HIS* 3.2 4.0 + - - +
73A CYS* 2.9 35.1 + - - -
96A LEU* 4.7 4.6 - - + +
100A GLY* 5.7 3.1 - - - -
132A SER* 3.2 28.7 - - - -
212A TRP* 3.8 11.1 - - + -
220A ILE* 4.7 1.3 - - + -
224A SER* 3.2 14.5 + - - -
225A MET* 4.4 3.8 - - + -
2001A B2A 4.2 0.9 + - - -
2002A B2A 2.9 51.5 + - + -
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Residues in contact with GLY 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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37A VAL* 3.9 3.5 - - - +
39A ASP* 3.1 27.2 + - - -
40A THR* 2.9 12.3 + - - -
41A GLY 3.1 21.1 - - - +
69A HIS* 1.3 75.1 - - - +
71A THR* 1.3 56.6 + - - +
73A CYS* 3.4 2.1 + - - +
74A ALA* 2.8 31.0 + - - +
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Residues in contact with THR 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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41A GLY 3.4 1.5 + - - -
42A ILE* 4.4 2.7 - - - +
43A GLU* 2.8 32.5 + - + +
46A HIS* 4.6 1.6 - - - +
49A PHE* 3.7 15.5 - - + -
65A ASP* 2.7 23.7 + - - -
68A GLY 3.1 5.1 + - - -
70A GLY* 1.3 77.5 - - - +
72A HIS* 1.3 56.3 + - - +
74A ALA* 4.4 4.3 - - - -
75A GLY 2.9 15.2 + - - -
211A THR* 2.8 26.3 + - - +
212A TRP* 3.7 31.2 - - - +
213A ILE* 3.7 5.2 - - - +
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Residues in contact with HIS 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 GLY 2.9 11.6 + - - +
69A HIS* 3.4 9.2 - - - +
71A THR* 1.3 75.5 - - - +
73A CYS* 1.3 63.5 + - - +
75A GLY 3.1 0.5 + - - -
76A THR* 3.0 10.1 + - - -
208A ILE* 2.9 33.7 + - + -
210A SER* 2.8 39.0 + - - -
211A THR 3.0 24.8 + - - +
212A TRP* 3.7 16.4 - + + -
218A ARG 2.9 20.2 + - - -
220A ILE* 3.5 27.8 - - + +
225A MET* 3.8 25.1 - - + +
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Residues in contact with CYS 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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37A VAL* 4.3 13.0 - - + -
39A ASP* 3.8 7.9 - - - +
69A HIS* 2.9 23.9 + - - +
70A GLY 3.8 3.8 - - - +
72A HIS* 1.3 77.3 - - - +
74A ALA* 1.3 62.9 + - - +
76A THR* 3.1 2.9 + - - -
77A VAL* 3.0 19.1 + - - +
130A SER* 5.6 1.3 - - - +
132A SER* 3.6 19.5 - - - +
224A SER 3.4 23.1 - - - -
225A MET* 3.8 15.5 - - - +
228A PRO* 3.3 23.7 - - + +
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Residues in contact with ALA 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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37A VAL* 4.0 17.0 - - + +
42A ILE* 3.8 29.8 - - + -
49A PHE* 3.8 14.8 - - + -
70A GLY 2.8 18.3 + - - +
71A THR 3.8 4.0 - - - +
73A CYS* 1.3 76.5 - - - +
75A GLY* 1.3 58.9 + - - +
77A VAL* 3.2 3.8 + - - +
78A GLY 2.9 24.4 + - - -
90A LEU* 3.8 11.2 - - + +
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Residues in contact with GLY 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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49A PHE* 3.7 2.8 - - - -
71A THR 2.9 11.7 + - - -
72A HIS 3.1 0.6 + - - -
74A ALA* 1.3 77.1 - - - +
76A THR* 1.3 58.5 + - - +
79A SER* 2.7 40.2 + - - -
82A TYR 3.3 0.8 - - - -
83A GLY* 3.1 6.4 + - - -
210A SER* 3.2 9.4 - - - -
211A THR* 3.2 21.1 - - - -
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Residues in contact with THR 76 (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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72A HIS* 3.0 14.6 + - - -
73A CYS 3.1 7.8 + - - -
75A GLY* 1.3 72.2 - - - +
77A VAL* 1.3 60.6 + - - +
82A TYR 3.5 11.3 + - - +
83A GLY* 3.2 0.3 - - - -
84A VAL* 2.9 28.6 + - - +
208A ILE* 3.9 12.5 - - + +
210A SER* 3.5 13.7 + - - -
225A MET* 3.9 1.9 + - - +
228A PRO* 3.8 11.0 - - + +
229A HIS* 3.4 54.5 - - + +
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Residues in contact with VAL 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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35A VAL* 3.7 37.5 - - + -
37A VAL* 4.3 11.2 - - + -
73A CYS 3.0 14.7 + - - +
74A ALA 3.2 6.7 + - - +
76A THR* 1.3 77.7 - - - +
78A GLY* 1.3 57.7 + - - +
84A VAL* 3.3 4.6 + - - +
85A ALA* 2.9 27.5 + - - +
88A THR* 4.2 3.6 - - + -
90A LEU* 3.6 19.5 - - + -
130A SER* 4.4 4.5 - - - +
228A PRO* 3.4 28.7 - - + +
231A ALA* 4.4 1.3 - - + -
232A GLY* 4.0 10.7 - - - -
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Residues in contact with GLY 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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52A ARG* 2.8 30.5 + - - -
74A ALA 2.9 10.3 + - - -
76A THR 3.4 0.6 - - - -
77A VAL* 1.3 79.3 - - - +
79A SER* 1.3 65.2 + - - +
83A GLY* 4.2 0.9 - - - -
85A ALA 3.3 17.7 - - - +
86A LYS 3.9 0.9 - - - +
88A THR* 4.1 10.3 - - - -
90A LEU* 4.2 9.4 - - - +
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Residues in contact with SER 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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48A GLU* 3.4 28.7 - - - -
49A PHE* 4.2 6.9 - - - -
52A ARG* 4.0 0.4 - - - +
74A ALA 3.8 1.6 + - - -
75A GLY* 2.7 35.2 + - - -
78A GLY* 1.3 80.3 - - - +
80A ARG* 1.3 67.1 + - - +
82A TYR* 3.0 26.2 + - - +
83A GLY* 3.0 16.1 + - - -
86A LYS* 3.6 6.3 - - - +
211A THR* 4.2 3.6 - - - -
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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