Contacts of the helix formed by residues 71 - 84 (chain A) in PDB entry 3RCL
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 VAL 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LYS* 2.8 15.6 + - + +
70A VAL* 1.3 81.9 - - + +
72A PRO* 1.3 60.4 - - - +
73A LYS 3.3 0.2 + - - -
74A THR* 3.3 3.8 + - - -
75A ALA* 2.9 26.7 + - - +
128A GLU* 3.2 20.6 - - + +
129A ASN* 3.4 34.8 - - - +
132A LEU* 4.7 0.4 - - + -
169A VAL* 4.1 17.5 - - + -
170A VAL 3.9 4.5 - - - +
171A PHE* 3.5 36.6 - - + -
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Residues in contact with PRO 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 ALA* 3.3 29.6 - - + +
69A ASP 4.7 1.6 - - - +
70A VAL 3.5 7.9 - - - +
71A VAL* 1.3 87.6 - - - +
73A LYS* 1.3 64.2 + - + +
75A ALA* 3.8 0.7 - - - +
76A GLU* 2.9 31.9 + - - +
128A GLU* 3.1 13.0 - - - +
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Residues in contact with LYS 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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72A PRO* 1.3 80.7 - - + +
74A THR* 1.3 61.7 + - - +
76A GLU* 4.5 0.4 - - - -
77A ASN* 3.2 10.2 + - - +
121A TYR* 2.6 42.7 + - + +
125A PHE* 4.6 7.0 - - + -
128A GLU* 2.9 30.7 + - + +
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Residues in contact with THR 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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71A VAL* 3.9 9.2 - - - -
73A LYS* 1.3 75.0 - - - +
75A ALA* 1.3 64.8 + - - +
77A ASN* 3.4 5.0 + - - +
78A PHE* 3.2 21.0 + - - +
125A PHE* 3.8 20.4 - - + -
128A GLU* 2.7 33.2 + - - +
142A MET* 3.7 27.4 - - + +
150A ASN* 6.0 0.6 - - - -
169A VAL* 4.0 10.1 - - + +
171A PHE* 3.7 27.3 - - + -
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Residues in contact with ALA 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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46A PRO* 5.3 3.6 - - + -
66A LEU* 3.5 24.7 - - + +
67A LYS 4.2 2.2 - - - +
68A ALA* 3.6 34.1 - - + +
71A VAL 2.9 18.2 + - - +
72A PRO 3.8 1.3 - - - +
74A THR* 1.3 77.4 - - - +
76A GLU* 1.3 56.6 + - - +
78A PHE 3.2 1.6 + - - -
79A ARG* 2.9 30.5 + - - +
171A PHE* 4.6 8.7 - - - +
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Residues in contact with GLU 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 PRO 2.9 19.9 + - - +
73A LYS* 4.5 0.7 - - - -
74A THR 3.3 0.2 - - - -
75A ALA* 1.3 76.2 - - - +
77A ASN* 1.3 64.6 + - - +
79A ARG* 2.9 45.3 + - - +
80A ALA* 3.0 26.7 + - - +
86A LYS* 4.9 5.9 + - - -
120A ILE* 4.0 10.6 - - + +
121A TYR* 3.7 16.2 - - + +
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Residues in contact with ASN 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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73A LYS 3.2 12.5 + - - +
74A THR 3.5 9.5 + - - +
76A GLU* 1.3 79.3 - - - +
78A PHE* 1.3 63.4 + - - +
80A ALA* 3.4 1.7 + - - +
81A LEU* 3.0 39.3 + - - +
90A TYR* 4.9 0.8 + - - -
119A SER* 3.3 4.1 - - - -
120A ILE* 2.8 42.3 + - - +
121A TYR* 3.8 9.6 + - + -
125A PHE* 3.6 18.8 - - + -
142A MET* 4.2 7.9 - - - +
151A GLY 3.0 25.7 + - - -
152A SER* 4.6 0.4 - - - +
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Residues in contact with PHE 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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48A VAL* 3.7 4.7 - - + -
50A LEU* 4.7 2.9 - - + -
64A LEU* 3.7 32.3 - - + -
66A LEU* 3.6 20.6 - - + -
74A THR 3.2 5.4 + - - +
75A ALA 3.7 6.3 - - - +
77A ASN* 1.3 81.9 - - - +
79A ARG* 1.3 63.2 + - - +
81A LEU* 3.3 3.2 + - - +
82A CYS* 3.0 47.8 + - - -
90A TYR* 3.3 38.8 - + - -
140A LEU* 4.4 1.8 - - + -
142A MET* 5.3 2.9 - - - -
154A PHE* 3.6 35.7 - + + -
171A PHE* 3.5 32.8 - + + -
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Residues in contact with ARG 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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46A PRO* 4.2 14.4 - - + -
48A VAL* 4.3 12.1 - - + -
66A LEU* 3.7 12.9 - - + +
75A ALA 2.9 18.1 + - - +
76A GLU* 2.9 43.6 + - - +
77A ASN 3.3 0.2 - - - -
78A PHE* 1.3 77.2 - - - +
80A ALA* 1.3 67.4 + - - +
82A CYS* 3.1 13.9 + - - +
83A THR* 3.1 22.6 + - - +
85A GLU* 2.9 42.8 + - - -
205A GLN* 3.0 45.6 + - + +
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Residues in contact with ALA 80 (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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76A GLU 3.0 17.2 + - - +
79A ARG* 1.3 92.5 - - - +
81A LEU* 1.3 58.1 + - - +
83A THR* 3.1 9.4 + - - -
84A GLY* 2.9 27.5 + - - -
85A GLU* 3.5 6.9 + - + -
86A LYS* 4.1 14.7 + - + +
88A PHE 4.4 1.0 - - - +
120A ILE* 3.8 28.7 - - + -
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Residues in contact with LEU 81 (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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77A ASN* 3.0 39.4 + - - +
78A PHE 3.7 0.2 - - - +
80A ALA* 1.3 75.5 - - - +
82A CYS* 1.3 62.1 + - - +
84A GLY* 3.7 3.5 + - - -
88A PHE* 3.7 37.2 - - + +
89A GLY* 3.3 11.9 - - - -
90A TYR* 3.0 60.9 + - + +
91A LYS 4.8 0.2 + - - -
109A PHE* 3.8 13.5 - - + -
118A LYS 4.1 2.5 - - - +
120A ILE* 4.1 9.6 - - + -
152A SER* 3.6 20.9 - - - -
203A CYS* 4.5 0.3 - - - -
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Residues in contact with CYS 82 (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* 4.0 14.4 - - + -
49A TYR 4.5 1.6 - - - -
50A LEU* 4.2 13.2 - - - -
78A PHE* 3.0 45.7 + - - -
79A ARG 3.1 8.9 + - - +
81A LEU* 1.3 77.1 - - - +
83A THR* 1.3 62.0 + - - +
84A GLY* 3.5 0.3 + - - -
90A TYR* 4.0 11.2 - - - -
91A LYS* 5.7 0.3 - - - +
203A CYS* 3.1 36.0 - - - +
204A GLY* 3.8 21.8 - - - +
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Residues in contact with THR 83 (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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79A ARG* 3.1 19.2 + - - +
80A ALA* 3.1 9.7 + - - -
82A CYS* 1.3 76.6 - - - +
84A GLY* 1.3 62.6 + - - +
85A GLU* 2.7 36.5 + - - +
203A CYS 4.9 1.0 - - - +
204A GLY* 4.3 4.5 - - - -
205A GLN* 3.8 31.6 - - + +
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Residues in contact with GLY 84 (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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80A ALA 2.9 6.6 + - - -
81A LEU 3.7 4.0 + - - -
82A CYS 3.3 3.6 - - - -
83A THR* 1.3 78.4 - - - +
85A GLU* 1.3 57.5 + - - +
86A LYS 3.2 2.9 - - - -
87A GLY* 3.0 23.6 + - - -
88A PHE 3.5 22.2 + - - -
89A GLY* 4.9 1.1 - - - -
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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