Contacts of the helix formed by residues 71 - 86 (chain A) in PDB entry 3V50
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 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 2.6 23.6 + - - +
69A MET 3.1 0.4 + - - -
70A SER* 1.3 78.7 - - - +
72A PHE* 1.3 61.5 + - - +
73A LYS 3.0 1.8 + - - -
74A VAL* 3.4 17.7 + - - +
75A VAL* 4.3 1.7 + - - +
186A MET* 4.5 7.4 - - - +
234A LYS* 3.6 27.8 - - - +
235A THR 3.9 13.2 + - - -
236A GLY* 3.9 4.0 - - - +
245A GLY* 4.3 6.3 - - - +
247A VAL* 4.1 19.1 - - + +
264A TYR* 2.8 34.9 + - + +
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 3.8 33.8 - - + +
69A MET 3.2 23.5 + - - +
70A SER* 3.0 2.0 - - - -
71A THR* 1.3 78.6 + - - +
73A LYS* 1.3 80.3 + - + +
75A VAL* 3.0 10.5 + - + +
76A LEU* 2.9 44.5 + - + -
135A ALA* 4.1 14.6 - - + -
139A LEU* 4.4 10.3 - - + -
148A LEU* 3.9 11.9 - - + -
162A LEU* 3.8 29.4 - - + -
166A GLU* 3.4 25.8 - - + -
169A LEU* 3.5 20.9 - - + -
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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
----------------------------------------------------------
70A SER* 3.4 15.7 - - - +
71A THR 3.0 1.4 - - - -
72A PHE* 1.3 93.0 - - + +
74A VAL* 1.3 60.7 + - - +
76A LEU* 3.5 9.8 - - + +
77A CYS* 3.1 27.0 + - - +
126A ALA* 3.4 24.9 - - + +
127A ILE* 3.9 14.9 - - + +
130A GLY 3.1 16.0 + - - -
131A ASP 3.4 4.6 + - - -
132A ASN* 2.8 28.6 + - - -
135A ALA* 3.8 18.8 - - + -
166A GLU* 3.6 15.0 - - - -
234A LYS* 4.1 4.5 - - - -
301A SA2 2.7 26.4 + - - +
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Residues in contact with VAL 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 THR 3.4 8.2 + - - +
72A PHE 3.1 0.8 - - - -
73A LYS* 1.3 75.5 - - - +
75A VAL* 1.3 65.0 + - - +
77A CYS 3.3 1.6 + - - -
78A GLY* 3.0 17.8 + - - -
127A ILE* 4.2 13.9 - - + -
190A LEU* 3.5 28.7 - - + -
193A LEU* 5.3 0.2 - - + -
194A LEU* 6.3 0.2 - - + -
207A LEU* 3.7 27.0 - - + +
211A MET* 4.0 27.1 - - + -
234A LYS* 3.5 33.4 - - + -
247A VAL* 4.5 4.7 - - + -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 5.7 2.0 - - - -
71A THR 5.1 1.3 - - - +
72A PHE* 3.0 11.0 + - + +
74A VAL* 1.3 76.0 - - - +
76A LEU* 1.3 62.8 + - - +
78A GLY* 3.1 2.8 + - - -
79A ALA* 3.0 18.5 + - - +
148A LEU* 3.9 16.3 - - + +
151A PHE* 4.3 6.9 - - + -
152A LEU* 3.7 35.4 - - + -
160A THR* 5.8 0.4 - - + -
186A MET* 4.0 29.8 - - + -
189A THR* 4.0 22.9 - - + -
190A LEU* 4.6 4.3 - - + -
193A LEU* 4.1 11.9 - - + -
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Residues in contact with LEU 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 PHE* 2.9 34.5 + - + +
73A LYS* 3.5 13.2 - - + +
75A VAL* 1.3 78.1 - - - +
77A CYS* 1.3 60.7 + - - +
79A ALA* 3.0 8.1 + - - +
80A VAL* 3.0 27.0 + - + +
126A ALA* 5.4 0.4 - - + -
135A ALA* 3.4 34.1 - - + +
138A LEU* 3.8 20.9 - - + +
139A LEU* 3.8 37.0 - - + +
142A VAL* 4.0 13.9 - - + -
148A LEU* 3.8 11.1 - - + +
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Residues in contact with CYS 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 3.1 13.2 + - - +
74A VAL 4.0 1.3 - - - +
76A LEU* 1.3 79.3 - - - +
78A GLY* 1.3 60.4 + - - +
80A VAL* 3.6 2.8 - - - +
81A LEU* 2.9 34.4 + - - +
123A CYS* 2.1 56.5 - - - -
126A ALA* 5.1 1.6 - - - -
127A ILE* 3.7 24.0 - - + -
138A LEU* 3.8 11.7 - - - -
207A LEU* 4.3 1.1 - - + -
210A TRP* 3.8 8.3 - - + -
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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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74A VAL 3.0 14.4 + - - -
75A VAL 3.1 5.1 + - - -
77A CYS* 1.3 77.5 - - - +
79A ALA* 1.3 56.1 + - - +
81A LEU* 3.3 3.4 + - - +
82A ALA* 3.0 27.9 + - - +
151A PHE* 3.9 6.9 - - - -
193A LEU* 4.2 19.5 - - - -
199A LEU* 3.8 10.5 - - - +
207A LEU* 4.2 10.4 - - - +
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Residues in contact with ALA 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 VAL 3.0 5.7 + - - -
76A LEU 3.0 9.2 + - - +
78A GLY* 1.3 72.9 - - - +
80A VAL* 1.3 65.8 + - - +
82A ALA* 3.2 4.2 + - - +
83A ARG* 3.1 24.8 + - - +
142A VAL* 4.0 17.5 - - + -
148A LEU* 3.7 15.9 - - + -
151A PHE* 3.7 39.5 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.0 15.3 + - + +
77A CYS* 3.6 13.0 - - - +
78A GLY 3.3 0.2 - - - -
79A ALA* 1.3 76.6 - - - +
81A LEU* 1.3 62.9 + - + +
83A ARG* 3.0 10.4 + - - +
84A VAL* 3.0 20.6 + - - +
89A GLU* 4.4 7.4 - - + -
91A LEU* 4.4 9.4 - - + -
119A VAL* 3.5 31.4 - - + -
123A CYS* 4.2 9.2 - - - -
138A LEU* 4.0 24.7 - - + -
141A THR* 4.4 5.4 - - - +
142A VAL* 3.9 18.8 - - + -
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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 CYS 2.9 22.0 + - - +
78A GLY 3.7 3.8 - - - +
79A ALA 3.3 0.2 - - - -
80A VAL* 1.3 71.9 - - + +
82A ALA* 1.3 61.9 + - - +
84A VAL* 3.1 7.3 + - + +
85A ASP* 2.9 31.9 + - - +
91A LEU* 4.0 30.7 - - + -
199A LEU* 4.1 10.8 - - + -
203A SER* 3.4 46.0 - - - +
206A GLN* 4.1 10.5 - - + -
207A LEU* 3.9 16.8 - - + +
210A TRP* 3.8 20.9 - - + -
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Residues in contact with ALA 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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78A GLY 3.0 14.6 + - - +
79A ALA 3.5 8.5 - - - +
80A VAL 3.2 0.4 - - - -
81A LEU* 1.3 75.0 - - - +
83A ARG* 1.3 62.9 + - + +
85A ASP* 3.3 6.3 + - - +
86A ALA* 3.1 23.4 + - - +
151A PHE* 3.7 23.1 - - + -
198A ARG 6.1 0.4 - - - +
199A LEU* 3.6 15.4 - - + +
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Residues in contact with ARG 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 ALA* 3.1 9.6 + - - +
80A VAL* 3.0 10.0 + - - +
82A ALA* 1.3 74.6 - - + +
84A VAL* 1.3 63.0 + - - +
86A ALA* 3.3 6.2 + - - -
87A GLY 3.1 3.3 + - - -
88A ASP* 2.8 60.8 + - + +
89A GLU* 3.1 34.0 + - + +
93A ARG* 4.7 2.8 - - - +
141A THR* 3.3 27.6 + - - +
142A VAL* 3.8 29.1 - - - +
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Residues in contact with VAL 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 VAL 3.0 19.8 + - - +
81A LEU* 3.1 12.5 + - + +
83A ARG* 1.3 75.2 - - - +
85A ASP* 1.3 67.6 + - - +
87A GLY* 3.0 14.7 + - - -
89A GLU* 3.4 34.4 - - + +
90A GLN* 4.6 1.1 - - - -
91A LEU* 3.9 43.5 - - + +
203A SER* 5.1 2.7 - - - +
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Residues in contact with ASP 85 (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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81A LEU 2.9 15.3 + - - +
82A ALA* 3.5 9.6 - - - +
84A VAL* 1.3 79.1 - - - +
86A ALA* 1.3 59.8 + - - +
87A GLY* 3.4 0.7 + - - -
198A ARG 4.4 2.5 - - - +
199A LEU* 3.4 14.4 - - - +
200A SER* 2.7 51.3 + - - -
203A SER* 2.7 13.9 + - - -
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Residues in contact with ALA 86 (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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82A ALA 3.1 16.0 + - - +
83A ARG* 3.7 4.7 - - - +
84A VAL 3.2 0.2 - - - -
85A ASP* 1.3 75.7 - - - +
87A GLY* 1.3 59.8 + - - +
88A ASP* 3.6 23.1 + - - +
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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
------------------------------------------------------------
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