Contacts of the helix formed by residues 51 - 68 (chain A) in PDB entry 2VN9
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 SER 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 LYS 3.6 2.6 + - - -
50A LEU* 1.3 75.7 - - - +
52A ALA* 1.3 55.6 + - - +
53A ARG* 3.7 9.8 + - - +
54A ASP* 3.0 35.5 + - - +
55A HIS* 2.8 32.7 + - - +
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Residues in contact with ALA 52 (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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50A LEU 3.9 0.6 + - - -
51A SER* 1.3 70.8 - - - +
53A ARG* 1.3 57.8 + - - +
55A HIS* 3.1 9.0 + - - +
56A GLN* 2.8 48.2 + - - +
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Residues in contact with ARG 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 SER* 3.2 9.9 + - - +
52A ALA* 1.3 78.9 - - - +
54A ASP* 1.3 62.8 + - - +
56A GLN* 3.3 24.5 + - - +
57A LYS* 3.3 28.7 + - + +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.9 27.6 - - + +
51A SER* 3.0 29.7 + - - +
53A ARG* 1.3 76.6 - - - +
55A HIS* 1.3 66.5 + - - +
57A LYS* 3.2 34.3 + - - +
58A LEU* 3.2 11.8 + - - +
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Residues in contact with HIS 55 (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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47A THR* 4.2 15.5 - - + -
50A LEU* 4.1 11.3 - - + +
51A SER 2.8 13.7 + - - +
52A ALA* 3.6 10.8 - - - +
54A ASP* 1.3 77.1 - - - +
56A GLN* 1.3 56.5 + - - +
58A LEU* 3.2 23.4 + - + +
59A GLU* 2.7 59.9 + - + +
86A HIS* 5.0 4.9 - + - -
1310A PO4 2.6 36.4 + - - -
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Residues in contact with GLN 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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52A ALA* 2.8 36.5 + - - +
53A ARG* 3.5 17.0 + - - +
54A ASP 3.2 0.4 - - - -
55A HIS* 1.3 76.9 - - - +
57A LYS* 1.3 57.8 + - - +
59A GLU* 3.4 25.0 + - - +
60A ARG* 3.0 28.5 + - - +
63A ARG* 5.3 1.2 + - - -
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Residues in contact with LYS 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 ARG* 3.3 25.8 + - - +
54A ASP* 3.2 25.2 + - - +
55A HIS 3.2 0.6 - - - -
56A GLN* 1.3 75.1 - - - +
58A LEU* 1.3 64.3 + - - +
60A ARG* 3.5 12.3 + - - +
61A GLU* 3.1 22.5 + - - +
159A GLY 5.4 8.7 - - - +
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Residues in contact with LEU 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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45A ILE* 3.8 36.8 - - + -
47A THR* 3.9 9.6 - - + -
50A LEU* 4.7 3.8 - - + -
54A ASP 3.2 7.4 + - - +
55A HIS* 3.2 36.9 + - + +
57A LYS* 1.3 78.5 - - - +
59A GLU* 1.3 64.0 + - - +
61A GLU* 3.2 10.3 + - - +
62A ALA* 3.0 22.6 + - - +
86A HIS* 3.9 33.0 - - + +
88A LEU* 4.2 15.5 - - + -
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Residues in contact with GLU 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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55A HIS* 2.7 50.7 + - + +
56A GLN* 3.5 26.2 + - - +
58A LEU* 1.3 75.5 - - - +
60A ARG* 1.3 56.7 + - - +
62A ALA* 3.5 5.7 + - - +
63A ARG* 3.0 43.1 + - - +
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Residues in contact with ARG 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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56A GLN 3.0 15.9 + - - +
57A LYS* 3.6 13.9 - - - +
58A LEU 3.2 0.4 - - - -
59A GLU* 1.3 73.5 - - - +
61A GLU* 1.3 60.0 + - - +
63A ARG* 3.3 21.9 + - - +
64A ILE* 2.9 42.5 + - + +
161A ALA 3.5 22.4 - - - -
162A ILE* 4.6 7.6 - - - +
163A GLU* 2.8 42.5 + - - +
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Residues in contact with GLU 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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43A LYS* 2.8 31.9 + - - +
57A LYS 3.1 14.0 + - - +
58A LEU* 3.7 10.7 - - - +
60A ARG* 1.3 79.2 - - - +
62A ALA* 1.3 58.4 + - - +
64A ILE* 3.8 4.4 - - - +
65A CYS* 2.9 37.4 + - - -
88A LEU* 3.7 19.3 - - + +
90A PHE* 4.4 6.9 - - - -
158A PHE 3.8 23.1 + - - +
159A GLY* 3.4 25.0 + - - -
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Residues in contact with ALA 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 LEU* 3.0 17.0 + - + +
59A GLU* 3.8 6.7 - - - +
61A GLU* 1.3 76.4 - - - +
63A ARG* 1.3 57.8 + - - +
65A CYS* 4.6 0.4 - - - -
66A ARG* 2.9 31.0 + - - +
76A LEU* 3.7 8.0 - - - +
79A SER* 3.7 25.6 - - - +
86A HIS* 4.8 4.3 - - + +
88A LEU* 3.8 18.5 - - + +
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Residues in contact with ARG 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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56A GLN 5.3 0.8 + - - -
59A GLU* 3.0 37.5 + - - +
60A ARG* 3.5 30.2 - - - +
62A ALA* 1.3 78.3 - - - +
64A ILE* 1.3 61.3 + - - +
66A ARG* 3.6 8.0 + - - +
67A LEU* 3.3 20.4 + - + +
163A GLU* 3.0 39.8 + - - +
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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 ARG* 2.9 36.6 + - + +
61A GLU* 3.8 5.2 - - - +
63A ARG* 1.3 71.4 - - - +
65A CYS* 1.3 63.6 + - - +
67A LEU* 3.1 19.6 + - - +
68A LEU* 3.3 28.1 - - + +
132A ILE* 3.9 19.2 - - + +
158A PHE* 3.9 22.7 - - + +
161A ALA* 3.5 36.1 - - + +
162A ILE 4.2 2.2 - - - +
163A GLU* 3.7 29.2 - - + -
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Residues in contact with CYS 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 GLU* 2.9 34.3 + - - +
62A ALA* 4.6 0.2 - - - -
64A ILE* 1.3 76.6 - - - +
66A ARG* 1.3 64.5 + - - +
67A LEU 3.3 0.3 + - - -
68A LEU* 3.3 23.2 + - - +
74A VAL 5.9 1.3 - - - +
75A ARG* 3.6 4.2 + - - -
76A LEU* 3.6 32.8 + - + +
90A PHE* 4.0 21.3 - - + -
158A PHE* 3.8 33.4 - - - -
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Residues in contact with ARG 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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62A ALA 2.9 19.0 + - - +
63A ARG* 3.7 7.6 - - - +
64A ILE 3.4 0.2 - - - -
65A CYS* 1.3 76.9 - - - +
67A LEU* 1.3 61.8 + - - +
75A ARG* 3.2 21.9 + - - +
76A LEU* 3.7 12.5 - - + +
79A SER* 6.2 3.4 - - - -
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Residues in contact with LEU 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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63A ARG* 3.3 10.5 + - + +
64A ILE* 3.1 13.0 + - - +
66A ARG* 1.3 80.5 - - - +
68A LEU* 1.3 60.2 + - - +
69A LYS* 3.6 6.9 + - - +
126A HIS* 5.2 1.2 + - - -
130A ASN* 3.7 34.8 - - + +
132A ILE* 3.5 26.2 - - + -
163A GLU* 5.7 4.7 - - + +
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Residues in contact with LEU 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* 3.3 23.1 - - + +
65A CYS* 3.3 10.9 + - - +
66A ARG 3.3 1.0 - - - -
67A LEU* 1.3 76.1 - - - +
69A LYS* 1.3 58.7 + - - +
70A HIS 4.2 0.9 - - - -
73A ILE* 4.1 19.9 - - + +
75A ARG* 3.1 24.5 + - - -
126A HIS* 4.2 11.0 - - + -
127A CYS* 4.1 18.6 - - - -
130A ASN* 4.0 17.5 - - + -
132A ILE* 3.6 21.3 - - + -
158A PHE* 3.4 45.5 - - + -
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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