Contacts of the helix formed by residues 63 - 79 (chain A) in PDB entry 3RZE
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 ASN 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.7 6.5 - - + +
58A LEU* 3.7 24.8 + - - +
60A THR* 3.1 36.4 + - - +
62A GLY* 1.4 76.5 - - - +
64A LEU* 1.4 58.1 + - - +
65A TYR 3.3 2.2 - - - -
66A ILE* 3.3 22.1 + - - +
67A VAL* 3.1 29.7 + - - +
125A ARG* 5.0 4.7 + - - -
416A GLN* 5.4 4.0 + - - +
472A ASN* 5.4 5.4 + - - +
475A PHE* 3.8 29.9 - - - -
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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
----------------------------------------------------------
52A VAL* 5.7 5.4 - - + -
53A ARG* 6.3 0.2 - - - +
59A HIS 5.9 0.7 - - - +
60A THR 3.6 6.9 + - - +
61A VAL* 3.3 19.2 + - - +
63A ASN* 1.4 76.2 - - - +
65A TYR* 1.4 57.6 + - + +
67A VAL* 3.4 17.7 - - + +
68A SER* 3.3 25.1 + - - -
141A LYS* 4.4 19.1 - - + -
144A ALA* 3.7 28.5 - - + -
145A SER* 4.2 15.9 - - - +
148A ILE* 4.4 21.6 - - + +
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Residues in contact with TYR 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 VAL* 3.6 23.6 - - + +
62A GLY* 3.7 11.4 - - - +
64A LEU* 1.4 75.2 - - + +
66A ILE* 1.3 63.2 + - - +
67A VAL 3.4 0.4 - - - -
68A SER* 4.0 5.3 + - - +
69A LEU* 3.5 20.1 + - - +
117A SER* 4.0 11.4 - - - +
120A ILE* 3.5 53.1 + - + +
121A LEU* 3.6 30.4 - - + +
124A ASP* 3.9 31.2 + - + +
127A ARG* 5.5 0.7 + - - -
143A ARG 4.5 1.0 + - - -
144A ALA* 3.7 21.4 - - + +
147A THR* 3.6 14.3 + - - -
148A ILE* 4.1 13.5 - - + -
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Residues in contact with ILE 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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48A VAL* 4.5 4.7 - - + +
62A GLY 3.6 14.8 - - - +
63A ASN* 3.3 22.6 + - - +
65A TYR* 1.3 77.8 - - - +
67A VAL* 1.4 57.7 + - - +
69A LEU* 3.7 7.2 + - + +
70A SER* 3.1 27.2 + - - -
121A LEU* 3.8 32.5 - - + -
125A ARG* 4.9 1.3 - - - +
416A GLN* 4.2 14.1 - - - +
420A ILE* 3.8 19.3 - - + -
468A TYR* 3.6 38.1 + - + -
475A PHE* 4.5 15.3 - - + -
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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
----------------------------------------------------------
48A VAL* 5.7 1.1 - - + +
49A LEU* 4.1 7.6 - - + -
52A VAL* 3.8 23.1 - - + -
53A ARG* 3.5 42.2 - - - +
63A ASN 3.1 18.1 + - - +
64A LEU* 3.4 21.1 - - + +
65A TYR 3.4 0.2 - - - -
66A ILE* 1.4 73.6 - - - +
68A SER* 1.4 59.9 + - - +
70A SER* 2.6 24.7 + - - +
71A VAL* 2.9 24.8 + - + +
148A ILE* 6.4 1.6 - - + -
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU 3.3 12.4 + - - -
65A TYR* 4.3 6.3 - - - -
66A ILE 3.6 0.2 - - - -
67A VAL* 1.4 77.2 - - - +
69A LEU* 1.3 56.4 + - - +
71A VAL* 3.4 11.2 + - - +
72A ALA* 3.1 24.6 + - - +
117A SER* 2.7 22.7 + - - -
120A ILE* 6.0 0.8 - - - +
148A ILE* 4.6 17.8 + - - +
151A ALA* 6.0 0.5 - - - +
152A TRP* 2.8 35.3 + - - +
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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
----------------------------------------------------------
65A TYR 3.5 15.9 + - - +
66A ILE* 3.9 8.1 - - + +
67A VAL 3.2 0.6 - - - -
68A SER* 1.3 77.9 - - - +
70A SER* 1.3 55.8 + - - +
72A ALA* 3.7 3.6 + - - +
73A ASP* 3.0 41.7 + - - +
114A SER* 3.4 40.6 - - - +
117A SER* 3.4 9.2 + - - -
118A VAL* 3.7 20.2 - - + -
121A LEU* 6.1 1.6 - - + -
420A ILE* 4.5 10.5 - - + -
424A PHE* 5.3 0.9 - - + -
464A ASN* 3.5 22.9 - - - +
468A TYR* 3.4 24.0 - - + +
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Residues in contact with SER 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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45A ASN* 3.3 31.7 - - - +
48A VAL* 3.9 22.1 - - - +
49A LEU* 3.5 16.2 + - - +
66A ILE 3.1 14.9 + - - -
67A VAL* 2.6 23.8 + - - -
69A LEU* 1.3 73.5 - - - +
71A VAL* 1.4 57.9 + - - +
73A ASP* 3.8 0.7 - - - -
74A LEU* 3.0 26.9 + - - +
468A TYR* 4.5 5.8 + - - -
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Residues in contact with VAL 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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49A LEU* 3.7 22.0 - - + -
53A ARG* 5.6 0.7 - - - +
67A VAL* 2.9 25.9 + - + +
68A SER* 3.5 10.8 - - - +
69A LEU 3.3 0.2 - - - -
70A SER* 1.4 73.0 - - - +
72A ALA* 1.4 58.9 + - - +
74A LEU* 2.9 23.6 + - - +
75A ILE* 3.0 31.7 + - + +
152A TRP* 3.7 22.0 - - + -
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Residues in contact with ALA 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 SER 3.1 14.0 + - - +
69A LEU 3.9 3.4 - - - +
71A VAL* 1.4 77.9 - - - +
73A ASP* 1.3 60.2 + - - +
75A ILE* 3.6 2.7 + - - +
76A VAL* 3.2 28.6 + - - +
110A ALA* 3.4 30.5 - - - +
113A ALA* 3.9 17.5 - - + -
114A SER* 3.5 14.1 - - - +
152A TRP* 4.0 8.5 - - + -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.7 1.6 - - - +
45A ASN* 3.2 28.2 + - - +
69A LEU* 3.0 26.3 + - - +
71A VAL 3.2 0.2 - - - -
72A ALA* 1.3 75.3 - - - +
74A LEU* 1.4 60.0 + - - +
76A VAL* 4.0 4.9 - - - +
77A GLY 3.5 8.1 + - - -
114A SER* 3.4 17.2 + - - -
460A ASN* 4.2 4.7 + - - -
461A SER* 2.6 51.2 + - - +
464A ASN* 3.6 28.2 + - - +
468A TYR* 5.0 0.2 + - - -
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Residues in contact with LEU 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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41A THR 4.0 7.2 - - - +
42A VAL* 3.4 36.6 - - + +
45A ASN* 4.1 9.9 - - + -
46A LEU* 3.8 26.7 - - + +
49A LEU* 4.1 12.3 - - + -
70A SER 3.0 16.2 + - - +
71A VAL* 2.9 8.9 + - - +
73A ASP* 1.4 74.6 - - - +
75A ILE* 1.4 62.8 + - + +
76A VAL 3.1 1.1 - - - -
77A GLY* 2.8 21.2 + - - -
78A ALA* 2.9 20.3 + - + +
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Residues in contact with ILE 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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71A VAL* 3.0 38.1 + - + +
72A ALA* 3.9 7.0 - - - +
74A LEU* 1.4 77.7 - - + +
76A VAL* 1.4 57.0 + - - +
78A ALA* 4.7 2.0 - - - +
79A VAL* 2.8 48.2 + - + +
80A VAL* 3.4 1.7 + - + -
106A MET* 3.9 35.4 - - + +
110A ALA* 3.7 23.1 - - + -
152A TRP* 5.3 6.1 - - + -
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Residues in contact with VAL 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 ALA 3.2 17.5 + - - +
73A ASP* 3.9 5.6 - - - +
74A LEU 3.1 0.4 - - - -
75A ILE* 1.4 76.1 - - - +
77A GLY* 1.3 53.6 + - - +
80A VAL* 3.7 13.7 - - + -
81A MET* 2.7 42.4 + - - +
107A ASP 5.8 0.9 - - - +
110A ALA* 3.8 20.9 - - + -
111A SER* 5.1 7.2 - - - +
457A GLY 5.7 0.2 - - - +
458A TYR* 3.7 33.2 - - + -
461A SER* 3.7 28.9 - - - +
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Residues in contact with GLY 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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38A CYS* 3.2 28.2 - - - -
41A THR* 4.0 16.4 - - - -
42A VAL* 3.4 14.2 - - - +
73A ASP 3.5 4.2 + - - -
74A LEU 2.8 13.4 + - - -
76A VAL* 1.3 76.3 - - - +
78A ALA* 1.3 55.3 + - - -
81A MET* 3.6 14.3 - - - +
82A PRO* 3.3 6.8 - - - +
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Residues in contact with ALA 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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42A VAL* 3.8 13.8 - - + +
74A LEU* 2.9 23.9 + - + +
75A ILE* 4.5 1.6 - - - +
77A GLY* 1.3 71.3 - - - +
79A VAL* 1.3 65.2 + - + +
82A PRO* 3.3 20.3 - - - +
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Residues in contact with VAL 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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75A ILE* 2.8 30.1 + - + +
78A ALA* 1.3 83.2 - - + +
80A VAL* 1.3 64.6 + - - +
81A MET 3.5 0.4 - - - -
82A PRO* 3.7 1.8 - - - -
83A MET* 3.4 45.9 + - + +
102A PHE* 5.7 3.4 - - + -
103A TRP* 3.6 6.6 - - + -
106A MET* 4.1 28.0 - - + -
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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
------------------------------------------------------------
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