Contacts of the helix formed by residues 54 - 67 (chain A) in PDB entry 2W77
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLN* 1.3 76.2 - - - +
55A LEU* 1.3 66.6 + - - +
56A GLY* 3.0 5.6 + - - +
57A SER* 3.1 18.0 + - - +
58A ALA* 3.0 19.8 + - - +
79A ASN 6.3 0.7 - - - +
80A LYS 3.8 7.4 - - - +
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Residues in contact with LEU 55 (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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53A GLN 3.3 2.1 + - - -
54A ALA* 1.3 70.4 - - - +
56A GLY* 1.3 56.4 + - - +
58A ALA* 3.3 4.3 + - + +
59A LEU* 2.9 45.2 + - + +
77A VAL* 3.6 45.8 + - + +
80A LYS* 3.1 35.3 + - + +
81A ARG 4.4 0.4 - - - +
82A SER* 4.6 4.9 - - - +
98A LEU* 4.2 11.7 - - + -
99A LEU* 3.7 28.0 - - + -
102A THR* 3.9 24.9 - - + +
104A ALA* 5.2 4.7 - - + -
115A ILE* 5.5 0.9 - - + -
117A VAL* 5.7 1.1 - - + -
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Residues in contact with GLY 56 (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 ALA* 3.0 5.8 + - - +
55A LEU* 1.3 73.4 - - - +
57A SER* 1.3 64.3 + - - -
59A LEU* 3.0 4.9 + - - +
60A GLN* 2.9 23.8 + - - +
72A TYR* 3.9 25.8 + - - -
77A VAL* 4.1 13.5 + - - +
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Residues in contact with SER 57 (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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53A GLN* 2.4 34.4 - - - +
54A ALA* 3.1 20.7 + - - +
56A GLY* 1.3 70.1 - - - +
58A ALA* 1.3 52.1 + - - +
60A GLN* 3.2 6.5 + - - +
61A GLU* 2.6 41.4 + - - +
343A ASP* 5.4 8.4 + - - -
405A ASN* 6.0 1.1 - - - +
407A ALA* 5.8 3.8 - - - -
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Residues in contact with ALA 58 (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 ILE* 4.1 12.1 - - + +
53A GLN* 3.4 11.6 + - + -
54A ALA 3.0 8.9 + - - +
55A LEU 3.4 9.2 - - - +
57A SER* 1.3 75.9 - - - +
59A LEU* 1.3 54.9 + - - +
61A GLU* 3.6 2.1 - - - +
62A PHE* 2.7 35.8 + - - +
82A SER* 3.4 36.6 - - - +
98A LEU* 4.0 12.1 - - + +
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Residues in contact with LEU 59 (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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55A LEU* 2.9 39.8 + - + +
56A GLY 3.0 4.5 + - - +
58A ALA* 1.3 75.1 - - - +
60A GLN* 1.3 65.0 + - - +
62A PHE* 3.1 4.9 + - + +
63A GLY* 3.0 21.1 + - - -
70A VAL* 4.0 25.7 - - + +
72A TYR* 3.8 43.7 - - + -
77A VAL* 4.1 6.7 - - + -
95A ILE* 4.0 25.4 - - + -
98A LEU* 4.4 10.1 - - + -
99A LEU* 4.5 1.3 - - + -
115A ILE* 4.0 16.8 - - + -
134A SER* 5.1 0.2 - - - -
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Residues in contact with GLN 60 (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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56A GLY 2.9 9.7 + - - +
57A SER* 3.5 10.1 - - - +
59A LEU* 1.3 79.4 - - - +
61A GLU* 1.3 61.3 + - - +
63A GLY* 3.4 1.0 + - - -
64A ARG* 3.3 23.9 + - - +
72A TYR* 3.3 26.1 + - - -
132A ILE* 4.2 3.9 - - - +
133A THR 2.8 11.0 + - - +
134A SER* 2.8 44.7 + - - +
136A GLN* 5.5 0.8 + - - -
405A ASN* 3.3 38.5 + - + +
409A GLY* 5.5 1.7 - - - +
411A VAL* 5.4 8.2 - - - +
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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
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49A ASP 4.3 4.5 - - - +
50A ILE* 3.9 9.9 - - + -
51A PRO* 4.0 13.2 - - - +
53A GLN* 2.7 37.2 + - - +
57A SER* 2.6 19.3 + - - +
58A ALA* 3.6 4.7 - - - +
60A GLN* 1.3 72.2 - - - +
62A PHE* 1.3 57.3 + - - +
64A ARG* 3.4 8.2 + - + +
65A GLN* 2.9 47.2 + - - +
342A PRO* 3.3 45.7 - - + +
343A ASP* 5.1 3.1 - - - +
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Residues in contact with PHE 62 (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 PHE* 3.6 35.4 - + - -
50A ILE* 3.6 10.3 - - + -
58A ALA 2.7 18.3 + - - +
59A LEU* 3.1 8.0 + - - +
61A GLU* 1.3 75.9 - - - +
63A GLY* 1.3 67.4 + - - +
65A GLN* 3.1 1.6 + - - +
66A ALA* 3.0 41.5 + - + +
68A ILE* 4.9 4.5 - - + -
70A VAL* 3.9 13.7 - - + -
85A ILE* 4.6 1.1 - - + -
91A PRO* 3.4 23.8 - - + -
94A ALA* 3.9 14.1 - - + -
95A ILE* 3.7 23.1 - - + -
98A LEU* 3.7 21.1 - - + -
113A ILE* 3.6 21.3 - - + -
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Residues in contact with GLY 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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59A LEU 3.0 11.5 + - - -
60A GLN 3.4 1.3 + - - -
62A PHE* 1.3 76.7 - - - +
64A ARG* 1.3 62.6 + - - +
66A ALA* 5.0 0.2 - - - -
67A ASP* 3.0 20.3 + - - -
68A ILE 3.1 30.0 + - - +
70A VAL* 3.6 13.0 - - - -
134A SER* 3.9 9.6 - - - -
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Residues in contact with ARG 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 GLN* 3.3 14.7 + - - +
61A GLU* 3.5 12.1 - - + +
62A PHE 3.1 0.6 - - - -
63A GLY* 1.3 78.6 - - - +
65A GLN* 1.3 63.6 + - + +
66A ALA 3.1 1.4 + - - -
67A ASP* 3.4 5.7 + - - +
134A SER* 5.1 2.6 + - - -
275A HIS* 2.9 21.7 + - + -
308A ARG* 4.6 13.5 - - - +
339A ASP* 4.3 21.4 + - - -
341A ASN 4.5 0.6 + - - -
342A PRO 3.2 26.7 + - - -
343A ASP* 4.2 1.4 - - - +
344A THR 4.0 9.9 - - - +
345A MET* 3.9 40.5 - - - +
403A GLU* 4.4 19.8 + - - -
405A ASN* 4.2 22.6 + - - +
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Residues in contact with GLN 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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46A VAL* 3.8 11.6 - - - +
47A GLU 4.5 8.5 - - - +
48A PHE* 3.7 15.8 - - + -
49A ASP* 2.9 44.0 + - - +
50A ILE* 3.4 21.9 - - + +
61A GLU* 2.9 28.5 + - - +
62A PHE 3.1 3.3 + - - +
64A ARG* 1.3 77.9 - - + +
66A ALA* 1.3 57.8 + - - +
67A ASP 3.5 0.2 - - - -
275A HIS* 3.6 35.4 - - + +
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Residues in contact with ALA 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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46A VAL* 4.7 10.8 - - + +
48A PHE* 3.7 23.8 - - + -
62A PHE* 3.0 31.6 + - + +
63A GLY 4.4 0.9 - - - +
65A GLN* 1.3 77.4 - - - +
67A ASP* 1.3 73.2 + - - +
68A ILE* 3.4 16.1 + - + +
91A PRO* 4.8 10.1 - - + +
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Residues in contact with ASP 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 GLY 3.0 7.5 + - - -
64A ARG 3.4 2.8 + - - +
66A ALA* 1.3 81.2 - - - +
68A ILE* 1.3 60.5 + - - +
111A ASN* 5.0 3.1 - - - +
140A ILE* 4.8 16.4 - - + +
273A PRO 4.7 2.6 - - - +
274A THR* 3.5 21.4 - - + +
275A HIS* 2.7 56.5 + - - +
276A GLU* 4.2 9.2 + - - +
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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