Contacts of the helix formed by residues 51 - 68 (chain A) in PDB entry 7V3X
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 GLY 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLY 3.4 2.9 - - - -
50A THR* 1.3 78.3 - - - +
52A LYS* 1.3 61.5 + - - +
53A THR 3.5 1.6 - - - -
54A LEU* 3.8 11.2 - - - +
55A PHE* 2.9 29.6 + - - +
207A LEU* 3.5 8.9 - - - +
239A ILE* 4.0 15.5 - - - -
244A ILE* 3.7 6.1 - - - +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.6 19.7 - - + +
45A SER 4.4 0.4 - - - -
46A GLY* 3.3 25.5 + - - +
47A THR 4.0 3.0 + - - -
48A SER* 4.6 3.2 - - - +
49A GLY 5.4 0.9 - - - +
50A THR* 3.5 16.8 - - - +
51A GLY* 1.3 74.8 - - - +
53A THR* 1.3 62.6 + - - +
55A PHE* 3.1 6.2 + - - +
56A SER* 3.0 30.5 + - - -
181A THR* 3.4 30.4 + - + +
182A THR 3.2 23.1 - - - +
183A GLU* 3.9 16.5 + - - +
207A LEU* 4.0 15.0 - - + -
199B PHE* 4.0 15.6 - - - -
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Residues in contact with THR 53 (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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51A GLY 3.5 0.2 - - - -
52A LYS* 1.3 76.9 - - - +
54A LEU* 1.3 57.1 + - - +
56A SER* 3.0 6.5 + - - -
57A ILE* 3.0 50.5 + - + +
73A PHE* 4.4 5.2 - - + -
78A GLU* 3.6 28.0 + - - +
83A ILE* 5.7 0.7 - - + -
145A ASP* 2.8 32.5 + - - +
226B ARG* 5.8 2.3 + - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY* 3.6 14.6 + - - +
52A LYS 3.2 0.6 - - - -
53A THR* 1.3 75.0 - - - +
55A PHE* 1.3 64.6 + - - +
57A ILE* 3.9 4.6 - - + +
58A GLN* 3.0 25.0 + - - +
90A PHE* 3.0 51.1 - - + -
92A TRP* 3.9 16.6 - - + -
239A ILE* 3.3 34.5 - - + -
243A GLY* 4.6 4.5 - - - -
244A ILE* 4.2 13.0 - - + -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 4.8 12.6 - - + -
25A ILE* 5.6 4.5 - - + -
28A PHE* 3.7 39.5 - + - -
36A LEU* 4.9 8.1 - - + -
44A VAL* 3.6 37.9 - - + -
51A GLY 2.9 19.6 + - - +
52A LYS* 3.3 7.6 - - - +
54A LEU* 1.3 76.8 - - - +
56A SER* 1.3 60.4 + - - +
58A GLN* 3.1 7.3 + - + +
59A PHE* 2.9 36.4 + - + -
179A VAL* 4.6 9.6 - - + -
205A VAL* 4.5 7.2 - - + -
207A LEU* 4.6 9.9 - - + -
220A LEU* 4.6 5.4 - - + -
244A ILE* 3.8 17.4 - - + +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS 3.0 12.6 + - - -
53A THR* 3.0 21.3 + - - -
55A PHE* 1.3 72.4 - - - +
57A ILE* 1.3 63.5 + - - +
59A PHE* 3.5 9.5 + - - +
60A LEU* 3.5 8.5 + - - +
73A PHE* 3.9 7.6 - - - -
143A SER* 2.8 40.3 + - - -
144A ILE 5.5 0.4 - - - -
145A ASP* 4.4 4.2 - - - +
179A VAL* 3.8 22.7 - - - -
181A THR* 4.0 8.6 + - - -
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Residues in contact with ILE 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 THR* 3.0 35.5 + - + +
54A LEU* 3.9 5.8 - - + +
56A SER* 1.3 75.6 + - - +
58A GLN* 1.3 57.4 + - - +
60A LEU* 3.2 7.5 + - - +
61A TYR* 3.0 28.2 + - + +
73A PHE* 3.6 24.7 - - + -
83A ILE* 3.4 40.8 - - + +
86A ASN* 6.2 1.3 - - + -
87A ALA* 4.7 5.4 - - + -
92A TRP* 4.0 24.0 - - + -
94A LEU* 4.3 17.7 - - + -
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Residues in contact with GLN 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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23A THR 4.3 0.6 - - - +
24A MET 5.0 0.6 + - - -
25A ILE* 4.2 16.2 - - + +
26A GLU 5.0 0.6 - - - +
54A LEU* 3.0 19.6 + - - +
55A PHE* 3.6 4.9 - - + +
57A ILE* 1.3 77.9 - - - +
59A PHE* 1.3 56.3 + - - +
61A TYR* 4.4 2.9 - - + -
62A ASN* 3.1 56.9 + - - +
92A TRP* 3.3 33.0 - - + -
242A HIS 4.2 8.5 + - - -
243A GLY* 3.5 4.3 - - - -
244A ILE* 3.0 49.3 + - - +
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Residues in contact with PHE 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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21A MET* 4.1 11.4 - - + -
23A THR* 4.2 13.7 - - + -
36A LEU* 3.4 31.2 - - + -
55A PHE* 2.9 20.3 + - + +
56A SER* 3.5 9.9 - - - +
57A ILE 3.2 0.2 - - - -
58A GLN* 1.3 76.9 - - - +
60A LEU* 1.3 61.7 + - + +
62A ASN* 4.4 0.3 - - - +
63A GLY 3.4 2.1 + - - -
141A ARG* 2.5 79.4 + - + +
142A VAL 3.7 13.2 - - - -
143A SER* 3.7 13.7 - - - -
177A THR* 4.1 17.0 - - + -
179A VAL* 3.3 26.7 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER 3.5 9.6 - - - +
57A ILE* 3.2 6.0 + - - +
59A PHE* 1.3 76.2 - - + +
61A TYR* 1.3 58.4 + - - +
63A GLY* 2.8 21.7 + - - -
64A ILE* 2.9 18.2 + - + +
69A GLU 4.6 0.5 - - - +
71A GLY* 3.8 18.8 - - - -
72A VAL 4.0 2.0 - - - +
73A PHE* 3.6 49.4 - - + +
103A LEU* 4.2 16.4 - - + -
141A ARG* 3.6 36.0 - - + +
142A VAL 4.1 0.4 - - - -
143A SER* 3.6 18.6 - - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.0 15.0 + - + +
58A GLN* 4.1 4.3 - - - +
60A LEU* 1.3 76.8 - - - +
62A ASN* 1.3 78.1 - - - +
64A ILE* 3.1 12.6 + - + +
65A ILE* 3.0 60.1 + - + +
91A GLY 5.3 0.3 + - - -
92A TRP* 3.4 65.8 - + + +
93A ASP 4.8 6.0 + - - -
94A LEU* 4.1 24.5 - - + -
97A LEU* 5.9 4.3 - - + -
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Residues in contact with ASN 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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23A THR 3.0 27.7 + - - +
24A MET* 3.1 33.2 + - + -
25A ILE* 3.6 1.6 - - - +
58A GLN* 3.1 35.3 + - - +
59A PHE 4.5 0.2 - - - +
61A TYR* 1.3 91.9 - - - +
63A GLY* 1.3 56.4 + - - +
65A ILE* 4.6 2.5 - - - +
66A GLU* 2.9 40.6 + - + +
67A PHE* 4.7 1.4 - - - -
92A TRP* 5.8 0.3 - - - -
141A ARG* 4.4 0.7 - - - -
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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 PHE 3.4 5.1 + - - -
60A LEU 2.8 16.6 + - - -
62A ASN* 1.3 73.9 - - - +
64A ILE* 1.3 55.6 + - - -
67A PHE* 3.5 8.2 + - - +
68A ASP 3.5 4.3 + - - -
69A GLU* 2.9 29.9 + - - +
141A ARG* 3.2 36.0 - - - +
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Residues in contact with ILE 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 LEU 2.9 18.8 + - - +
61A TYR* 3.1 10.1 + - + +
63A GLY* 1.3 74.3 - - - +
65A ILE* 1.3 76.9 + - + +
68A ASP* 2.7 28.6 + - - +
69A GLU 3.4 20.4 - - - +
71A GLY* 4.3 4.5 - - - +
94A LEU* 6.5 0.4 - - + -
97A LEU* 4.6 10.1 - - + -
102A LYS* 3.4 57.6 - - + +
103A LEU* 3.6 28.5 - - + -
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Residues in contact with ILE 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 TYR* 3.0 54.8 + - + +
62A ASN* 4.6 2.2 - - - +
64A ILE* 1.3 88.2 - - + +
66A GLU* 1.3 63.7 + - + +
68A ASP 5.0 0.2 + - - -
97A LEU* 5.8 5.4 - - + -
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Residues in contact with GLU 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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24A MET* 3.8 38.2 - - + +
62A ASN* 2.9 20.3 + - + +
65A ILE* 1.3 82.3 - - + +
67A PHE* 1.3 83.9 + - + +
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Residues in contact with PHE 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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22A ARG* 3.5 48.7 - - + -
24A MET* 3.8 22.7 - - + -
62A ASN 4.9 1.6 - - - -
63A GLY* 3.5 12.0 + - - +
66A GLU* 1.3 110.3 - - + +
68A ASP* 1.3 72.5 + - - +
69A GLU* 3.4 22.2 + - + +
141A ARG* 3.4 18.4 - - - -
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Residues in contact with ASP 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 ILE* 2.7 26.4 + - - +
65A ILE 4.7 0.2 - - - -
66A GLU 4.0 0.6 - - - -
67A PHE* 1.3 74.5 - - - +
69A GLU* 1.3 58.3 + - - +
70A PRO* 3.6 10.5 - - - +
102A LYS* 4.4 22.2 + - - +
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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
------------------------------------------------------------
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