Contacts of the helix formed by residues 60 - 72 (chain A) in PDB entry 1GEY
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 PRO 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO* 5.8 1.8 - - + -
57A GLU* 3.8 29.3 - - + +
58A CYS 4.0 2.5 - - - +
59A GLN* 1.3 81.7 - - - +
61A LYS* 1.3 67.2 + - - +
62A ALA* 3.3 2.0 - - + +
63A VAL* 3.1 22.9 + - + +
64A ILE* 3.1 24.3 + - - +
80A VAL* 3.9 18.2 - - + -
245A LEU* 4.3 15.5 - - + +
250A ALA* 3.6 24.7 - - + -
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Residues in contact with LYS 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 GLU* 3.2 25.4 + - - +
59A GLN 3.1 6.8 + - - -
60A PRO* 1.3 70.3 - - - +
62A ALA* 1.3 79.0 + - - +
64A ILE* 3.5 4.3 + - - +
65A GLU* 3.1 58.5 + - + +
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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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57A GLU* 4.9 1.0 + - - -
60A PRO* 3.3 1.5 - - + -
61A LYS* 1.3 93.9 - - - +
63A VAL* 1.3 62.7 + - + +
65A GLU* 4.9 2.9 - - - -
66A ASN* 3.2 34.6 + - - +
250A ALA 5.7 0.2 - - - +
254A ALA* 4.0 19.5 - - + -
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Residues in contact with VAL 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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60A PRO* 3.1 28.2 + - + +
62A ALA* 1.3 76.8 - - + +
64A ILE* 1.3 60.2 + - + +
66A ASN* 3.6 3.1 + - - +
67A TYR* 3.0 30.5 + - - +
80A VAL* 4.1 13.7 - - + -
223A CYS* 4.9 0.2 - - - -
225A PHE* 3.7 28.7 - - + -
245A LEU* 5.0 1.6 - - + -
250A ALA* 3.4 33.4 - - + +
253A ALA* 4.2 16.4 - - + -
254A ALA* 4.4 6.5 - - + +
257A LEU* 4.1 4.3 - - + +
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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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59A GLN* 3.8 24.0 - - + +
60A PRO 3.1 19.8 + - - +
61A LYS* 4.0 4.7 - - - +
63A VAL* 1.3 75.5 - - - +
65A GLU* 1.3 60.2 + - + +
67A TYR* 4.2 1.0 - - - +
68A ALA* 3.1 25.8 + - - +
75A PRO* 3.4 34.5 - - + +
78A VAL* 3.9 25.2 - - + +
80A VAL* 3.8 37.7 - - + +
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Residues in contact with GLU 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 LYS* 3.1 49.2 + - + +
62A ALA* 4.4 3.2 + - - +
64A ILE* 1.3 79.1 - - + +
66A ASN* 1.3 67.2 + - - +
67A TYR 3.2 0.2 - - - -
68A ALA* 3.4 6.1 + - - +
69A GLN* 3.1 33.0 + - - +
75A PRO* 4.5 21.6 - - + +
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Residues in contact with ASN 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* 3.2 25.8 + - - +
63A VAL* 4.1 1.8 - - - +
65A GLU* 1.3 80.1 - - - +
67A TYR* 1.3 62.1 + - - +
69A GLN* 3.5 12.0 + - - +
70A TYR* 3.2 22.2 + - - +
254A ALA* 3.2 30.9 + - - +
257A LEU* 3.6 33.6 + - + +
258A SER* 4.3 5.1 - - - +
259A PRO* 5.9 1.3 - - - +
262A ILE* 4.9 0.9 - - - +
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Residues in contact with TYR 67 (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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63A VAL 3.0 18.6 + - - +
64A ILE 4.2 2.9 - - - +
66A ASN* 1.3 77.5 - - - +
68A ALA* 1.3 58.5 + - - +
70A TYR* 3.3 24.6 + + - +
71A ALA* 2.9 43.5 + - + +
78A VAL* 4.3 4.9 - - + -
189A GLU* 4.4 2.6 + - - -
210A ARG* 2.9 42.8 + - + +
211A THR 4.7 2.3 + - - -
212A LEU* 4.5 6.3 - - + -
216A PHE* 4.9 1.8 - + - -
225A PHE* 3.7 49.4 - + + -
227A LEU* 4.0 21.8 - - + -
257A LEU* 3.7 23.5 - - + +
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Residues in contact with ALA 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 3.1 19.5 + - - +
65A GLU 3.8 4.7 - - - +
66A ASN 3.3 0.2 - - - -
67A TYR* 1.3 77.9 - - - +
69A GLN* 1.3 57.2 + - + +
72A GLY* 2.9 7.6 + - - -
73A VAL* 2.9 53.1 + - - +
75A PRO* 3.8 26.9 - - + -
78A VAL* 3.9 7.8 - - + +
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Residues in contact with GLN 69 (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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65A GLU* 3.1 23.8 + - - +
66A ASN* 3.8 11.7 + - - +
67A TYR 3.2 0.2 - - - -
68A ALA* 1.3 73.5 - - + +
70A TYR* 1.3 67.0 + - - +
72A GLY* 3.5 8.9 + - - -
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Residues in contact with TYR 70 (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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66A ASN 3.2 12.7 + - - +
67A TYR* 3.5 40.6 - + - +
69A GLN* 1.3 81.6 - - - +
71A ALA* 1.3 63.7 + - - +
72A GLY* 3.2 1.4 + - - -
188A ILE* 5.5 0.5 - - - +
189A GLU* 2.7 40.9 + - - +
210A ARG* 4.1 9.0 + - - -
216A PHE* 4.0 8.3 - + - -
257A LEU* 4.8 3.4 - - + -
262A ILE* 3.7 41.2 - - + +
265A MET* 3.4 22.8 - - + +
266A ARG* 4.4 14.1 + - - -
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Residues in contact with ALA 71 (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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67A TYR* 2.9 41.4 + - + +
70A TYR* 1.3 76.2 - - + +
72A GLY* 1.3 62.6 + - - +
73A VAL* 3.6 13.1 + - + +
197A ALA* 4.3 11.4 - - - +
210A ARG* 3.9 18.1 + - - +
227A LEU* 4.0 14.1 - - + -
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Residues in contact with GLY 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 2.9 8.3 + - - -
69A GLN* 3.5 6.7 + - - -
70A TYR 3.2 4.8 + - - -
71A ALA* 1.3 81.4 - - - +
73A VAL* 1.3 62.0 + - - +
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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