Contacts of the helix formed by residues 50 - 65 (chain A) in PDB entry 2Y60
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLY 3.9 2.0 + - - -
49A ILE* 1.3 76.4 - - - +
51A VAL* 1.3 55.7 + - - +
52A GLN* 3.4 10.3 + - - +
53A ARG* 3.0 42.2 + - + +
54A LEU* 3.1 24.3 + - - +
141A PHE* 5.5 0.9 - - - -
148A ASP* 5.8 0.6 + - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A HIS* 3.9 5.2 - - + +
49A ILE* 3.0 16.9 + - + +
50A ASN* 1.3 71.3 - - - +
52A GLN* 1.3 68.8 + - + +
54A LEU* 3.5 7.1 - - + +
55A SER* 3.0 23.7 + - - -
224A TYR* 3.7 23.6 - - + -
246A ASP 3.5 24.2 - - - +
247A THR* 4.1 16.6 - - - +
248A GLY 5.3 0.4 - - - +
249A TYR* 3.5 42.0 - - + +
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Residues in contact with GLN 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 ASN* 3.3 7.9 + - - +
51A VAL* 1.3 82.8 - - + +
53A ARG* 1.3 67.1 + - - +
55A SER* 2.7 26.8 + - - +
56A GLN* 2.9 29.2 + - - +
224A TYR* 5.6 0.4 - - - -
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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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50A ASN* 3.0 36.8 + - + +
52A GLN* 1.3 82.1 + - - +
54A LEU* 1.3 66.9 + - - +
56A GLN* 3.7 5.3 - - + +
57A LYS* 2.9 66.8 + - + +
141A PHE* 3.5 17.2 - - + +
1335A SO4 2.9 43.6 + - - -
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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
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50A ASN 3.1 14.9 + - - +
51A VAL* 3.5 9.9 - - - +
53A ARG* 1.3 76.5 - - - +
55A SER* 1.3 61.1 + - - +
57A LYS* 4.0 0.7 - - - +
58A THR* 2.9 41.9 + - - +
141A PHE* 3.5 21.2 - - + -
145A TYR* 3.6 58.8 - - + +
186A LEU* 4.7 5.4 - - + -
224A TYR* 4.2 17.5 - - + -
249A TYR* 3.8 8.1 - - - +
282A LEU* 3.6 23.1 - - + -
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Residues in contact with SER 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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51A VAL 3.0 14.9 + - - -
52A GLN* 2.7 25.9 + - - +
54A LEU* 1.3 79.1 - - - +
56A GLN* 1.3 57.8 + - - +
58A THR* 4.5 1.1 - - - -
59A LYS* 2.8 27.6 + - - +
224A TYR* 3.5 19.2 + - - -
280A GLN* 3.0 31.1 + - - +
282A LEU* 4.8 0.2 - - - -
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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 GLN* 2.9 29.0 + - - +
53A ARG* 3.1 8.0 + - + +
55A SER* 1.3 82.8 + - - +
57A LYS* 1.3 63.2 + - + +
59A LYS* 3.3 21.5 + - - +
60A GLU* 2.9 64.1 + - - +
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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* 2.9 59.3 + - + +
56A GLN* 1.3 79.2 - - + +
58A THR* 1.3 62.0 + - - +
60A GLU* 3.4 26.0 + - - +
61A PHE* 3.1 22.9 + - - +
137A GLY 6.5 0.7 - - - -
138A PHE* 4.5 8.8 - - + -
141A PHE* 3.6 43.1 - - + -
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Residues in contact with THR 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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54A LEU* 2.9 36.1 + - - +
57A LYS* 1.3 73.7 - - - +
59A LYS* 1.3 60.8 + - - +
61A PHE* 3.2 6.8 + - + +
62A HIS* 2.9 56.2 + - + +
138A PHE* 5.3 1.1 - - - -
141A PHE* 5.0 2.3 - - - -
186A LEU* 3.8 23.5 - - + +
280A GLN* 3.8 12.8 - - - +
282A LEU* 3.9 19.5 - - + +
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Residues in contact with LYS 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 SER 2.8 19.4 + - - +
56A GLN* 3.5 23.1 + - - +
58A THR* 1.3 76.4 - - - +
60A GLU* 1.3 57.3 + - - +
62A HIS* 3.3 4.9 + - - +
63A MET* 2.9 55.1 + - + +
280A GLN* 3.3 11.8 - - - +
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Residues in contact with GLU 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* 2.9 52.5 + - - +
57A LYS* 3.7 27.4 + - - +
58A THR 3.3 0.2 - - - -
59A LYS* 1.3 77.1 - - + +
61A PHE* 1.3 55.0 + - - +
63A MET* 4.0 2.3 - - - +
64A SER* 2.8 36.7 + - - -
135A HIS* 5.5 0.2 - - - -
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Residues in contact with PHE 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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57A LYS 3.1 6.2 + - - +
58A THR 3.5 7.4 - - - +
60A GLU* 1.3 77.0 - - - +
62A HIS* 1.3 83.1 + + - +
64A SER* 3.2 5.1 + - - -
65A ILE* 3.0 55.0 + - + +
73A LEU* 5.3 0.2 - - + -
90A TYR* 4.0 10.5 - + - -
103A PHE* 3.7 41.3 - + + -
130A PRO* 4.0 12.6 - - + -
135A HIS* 3.8 18.6 - + - +
138A PHE* 3.6 48.5 - + + -
186A LEU* 4.5 5.6 - - + -
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Residues in contact with HIS 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 THR* 2.9 43.5 + - + +
59A LYS* 4.0 3.8 - - - +
61A PHE* 1.3 87.7 - + - +
63A MET* 1.3 69.0 + - - +
64A SER 3.5 0.3 + - - -
65A ILE* 3.5 19.1 - - - +
70A LYS* 5.5 1.0 + - - -
90A TYR* 4.0 17.3 + + - -
101A GLU* 4.8 2.6 + - - +
102A SER* 4.8 0.8 - - - -
186A LEU* 2.9 32.4 + - - +
187A ILE 3.6 7.4 - - - -
188A ARG* 3.5 55.7 + - + +
280A GLN* 4.8 7.7 + - + +
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Residues in contact with MET 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 LYS* 2.9 42.9 + - + +
60A GLU* 4.4 3.4 - - - +
62A HIS* 1.3 82.8 - - + +
64A SER* 1.3 59.0 + - - +
65A ILE 4.9 1.8 - - - +
188A ARG* 3.6 40.4 - - - +
278A GLU* 4.4 15.3 - - + +
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Residues in contact with SER 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 GLU 2.8 20.6 + - - -
61A PHE 3.2 0.8 + - - -
63A MET* 1.3 79.6 - - - +
65A ILE* 1.4 66.3 - - - +
66A THR* 3.5 12.8 + - - +
69A GLU* 4.0 2.1 - - - +
134A LYS 4.8 3.4 + - - -
135A HIS* 3.1 24.4 + - - -
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A PHE* 3.0 31.5 + - + +
62A HIS* 3.5 21.4 - - - +
63A MET 4.9 1.6 - - - +
64A SER* 1.4 78.5 + - - +
66A THR* 1.3 66.3 + - - +
67A PRO* 4.7 0.9 - - - +
69A GLU* 3.5 28.9 - - + +
70A LYS* 3.7 29.6 + - + +
73A LEU* 4.2 11.7 - - + -
90A TYR* 3.7 39.0 - - + +
130A PRO* 5.4 0.4 - - + -
135A HIS* 3.9 8.3 - - + +
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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