Contacts of the helix formed by residues 55 - 71 (chain A) in PDB entry 1R6W
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 THR 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A PRO* 3.7 3.4 - - - -
53A GLN 4.9 3.8 - - - +
54A GLU* 1.3 76.6 - - - +
56A TRP* 1.3 65.0 + - - +
57A GLU* 3.5 19.6 + - - +
58A GLU* 3.0 39.0 + - - +
59A ALA* 2.9 23.2 + - - +
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Residues in contact with TRP 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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8A ARG* 3.3 35.2 - - + +
9A TRP 3.5 14.6 - - - -
10A GLN* 3.8 26.9 - - + -
28A ASP* 3.5 34.1 - - + +
29A GLY* 3.1 31.6 + - - +
30A LEU* 3.8 19.2 - - + +
45A ILE 5.2 0.9 - - - -
47A PRO* 3.7 17.4 - - + +
55A THR* 1.3 71.6 - - - +
57A GLU* 1.3 74.8 + - + +
59A ALA* 3.3 2.6 + - - +
60A GLN* 2.9 28.0 + - - +
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Residues in contact with GLU 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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55A THR* 3.2 18.3 + - - +
56A TRP* 1.3 99.8 - - + +
58A GLU* 1.3 62.7 + - + +
60A GLN* 3.4 12.7 + - - +
61A SER* 3.1 21.8 + - - -
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Residues in contact with GLU 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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53A GLN 4.2 2.6 - - - +
54A GLU* 3.4 9.8 - - + +
55A THR* 3.0 42.1 + - - +
57A GLU* 1.3 72.8 - - + +
59A ALA* 1.3 66.3 + - - +
61A SER* 3.4 7.0 + - - -
62A VAL* 3.1 27.0 + - - +
80A MET* 4.0 16.3 - - + +
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Residues in contact with ALA 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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30A LEU* 4.1 3.1 - - + -
45A ILE* 3.9 10.3 - - + -
47A PRO* 4.0 9.4 - - + -
54A GLU* 4.5 0.2 - - + -
55A THR 2.9 16.1 + - - +
56A TRP 3.6 4.5 - - - +
58A GLU* 1.3 76.8 - - - +
60A GLN* 1.3 59.9 + - - +
62A VAL 3.3 0.7 + - - -
63A LEU* 2.8 32.1 + - - +
80A MET* 3.7 13.4 - - - -
82A SER* 3.8 22.4 - - - +
83A VAL* 3.6 10.2 - - + +
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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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6A VAL* 5.7 0.4 - - + -
8A ARG* 3.1 43.7 + - - +
30A LEU* 3.6 19.8 - - + +
56A TRP* 2.9 17.2 + - - +
57A GLU* 3.5 15.6 - - - +
59A ALA* 1.3 77.3 - - - +
61A SER* 1.3 56.4 + - - +
63A LEU* 3.7 2.4 - - - +
64A LEU* 3.0 42.3 + - + +
319A LEU* 3.5 26.3 - - + +
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Residues in contact with SER 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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57A GLU 3.1 10.4 + - - -
58A GLU* 3.6 11.7 - - - -
59A ALA 3.3 0.2 - - - -
60A GLN* 1.3 81.9 - - - +
62A VAL* 1.3 65.5 + - - +
64A LEU* 3.9 6.2 - - - +
65A ALA* 3.1 24.1 + - - +
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Residues in contact with VAL 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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58A GLU* 3.1 17.1 + - + +
59A ALA 3.9 3.1 - - - +
61A SER* 1.3 78.5 - - - +
63A LEU* 1.3 57.7 + - - +
65A ALA* 3.4 5.6 + - - +
66A TRP* 3.0 27.1 + - + +
78A PRO* 4.2 15.7 - - + -
80A MET* 3.6 30.5 - - + +
83A VAL* 4.0 19.7 - - + -
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Residues in contact with LEU 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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6A VAL* 3.7 33.9 - - + -
30A LEU* 4.2 17.9 - - + -
31A TYR 4.5 0.4 - - - +
32A VAL* 4.0 17.9 - - + -
45A ILE* 3.8 24.7 - - + -
59A ALA 2.8 19.0 + - - +
60A GLN* 3.7 3.6 - - - +
62A VAL* 1.3 75.8 - - - +
64A LEU* 1.3 65.7 + - - +
66A TRP* 3.2 2.3 + - + -
67A VAL* 2.9 34.8 + - + +
83A VAL* 3.9 12.3 - - + +
87A VAL* 3.6 31.2 - - + -
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Residues in contact with LEU 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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6A VAL* 3.9 29.4 - - + -
60A GLN* 3.0 45.8 + - + +
61A SER* 3.9 5.8 - - - +
63A LEU* 1.3 76.2 - - - +
65A ALA* 1.3 62.1 + - - +
67A VAL* 3.4 4.7 + - - +
68A ASN* 3.0 24.1 + - - +
319A LEU* 4.3 13.7 - - + +
320A LEU* 3.7 32.2 - - + +
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Residues in contact with ALA 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 SER* 3.1 18.1 + - - +
62A VAL* 3.8 5.8 - - - +
64A LEU* 1.3 76.4 - - - +
66A TRP* 1.3 64.8 + - - +
68A ASN* 3.3 9.8 + - - +
69A ASN* 3.2 27.6 + - - +
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Residues in contact with TRP 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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32A VAL* 5.4 0.2 - - + -
34A LEU* 3.8 29.2 - - + -
62A VAL* 3.0 17.9 + - + +
63A LEU* 3.7 5.6 - - - +
65A ALA* 1.3 78.2 - - - +
67A VAL* 1.3 66.3 + - + +
69A ASN* 3.0 9.9 + - - +
70A TRP* 2.9 62.6 + + + -
75A CYS* 3.4 20.4 - - - -
76A GLU 3.1 27.7 + - - -
77A LEU* 4.0 3.0 - - + +
78A PRO* 3.4 30.6 - - + +
87A VAL* 3.2 44.2 - - + -
91A LEU* 3.9 12.3 - - + -
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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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4A ALA* 3.5 28.9 - - + -
6A VAL* 4.1 7.9 - - + -
32A VAL* 3.8 27.6 - - + -
34A LEU* 4.5 2.7 - - + -
63A LEU* 2.9 23.8 + - + +
64A LEU* 3.7 6.3 - - - +
66A TRP* 1.3 91.9 - - + +
68A ASN* 1.3 62.7 + - - +
70A TRP* 3.2 1.7 + - - +
71A LEU* 3.0 31.3 + - + +
320A LEU* 3.9 19.5 - - + -
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Residues in contact with ASN 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 LEU 3.0 14.3 + - - +
65A ALA* 3.5 12.0 - - - +
67A VAL* 1.3 77.8 - - - +
69A ASN* 1.3 64.0 + - - +
71A LEU* 3.9 19.3 + - - +
72A ALA* 4.1 6.4 + - - +
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Residues in contact with ASN 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 ALA* 3.2 18.8 + - - +
66A TRP* 3.0 10.5 + - + +
68A ASN* 1.3 78.2 + - - +
70A TRP* 1.3 65.4 + - - +
72A ALA* 2.9 18.7 + - - +
73A GLY 3.2 11.4 + - - +
75A CYS* 3.9 19.9 - - + +
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Residues in contact with TRP 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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2A ARG* 2.9 74.5 + - + +
3A SER 3.6 20.2 - - - -
4A ALA* 4.8 0.4 - - + -
34A LEU* 3.8 33.2 - - + -
35A ARG 3.5 20.0 - - - -
36A GLU* 4.5 2.9 - - + -
66A TRP* 2.9 50.4 + + + +
67A VAL* 3.8 4.0 - - - +
69A ASN* 1.3 76.4 - - - +
71A LEU* 1.3 75.4 + - + +
73A GLY 3.0 11.1 + - - -
74A ASP* 4.2 11.4 + - - -
75A CYS* 3.9 3.8 - - - -
91A LEU* 3.6 16.0 - - + +
94A LEU* 3.6 22.4 - - + -
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Residues in contact with LEU 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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2A ARG* 3.8 25.9 - - - +
3A SER* 3.5 41.1 - - - +
4A ALA* 3.9 7.9 - - + +
67A VAL* 3.0 34.5 + - + +
68A ASN* 4.0 14.1 - - - +
69A ASN 3.1 0.2 - - - -
70A TRP* 1.3 83.5 - - + +
72A ALA* 1.3 58.9 + - - +
320A LEU* 5.4 5.6 - - + -
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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