Contacts of the helix formed by residues 60 - 72 (chain A) in PDB entry 5YFG
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ARG* 1.3 72.0 - - - +
61A GLU* 1.3 67.0 + - - -
62A ALA 3.1 1.6 - - - -
63A ALA* 3.0 14.1 + - - +
64A ALA* 3.1 12.3 + - - +
101A GLU* 5.7 2.2 - - - -
102A ALA* 5.8 0.7 - - - -
103A TRP* 3.2 30.2 - - - +
128A LEU* 4.0 9.6 + - - +
130A ARG* 4.6 9.4 - - - +
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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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59A ARG 3.7 0.4 + - - -
60A GLY* 1.3 70.6 - - - -
62A ALA* 1.3 60.8 + - - +
64A ALA* 3.4 4.6 + - + +
65A ARG* 3.0 60.1 + - - +
85A VAL* 3.5 24.9 - - + +
103A TRP* 3.5 44.6 - - + +
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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 HIS 5.8 0.7 - - - +
58A VAL* 3.5 12.5 - - + +
59A ARG 3.6 12.3 + - - +
60A GLY 3.1 0.6 - - - -
61A GLU* 1.3 76.9 - - - +
63A ALA* 1.3 58.6 + - - +
65A ARG* 3.5 6.3 + - - +
66A TYR* 2.9 31.4 + - - +
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Residues in contact with ALA 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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58A VAL* 3.4 19.4 - - - +
59A ARG* 3.3 28.7 + - - -
60A GLY 3.0 9.7 + - - +
62A ALA* 1.3 80.0 - - - +
64A ALA* 1.3 56.3 + - - +
67A HIS* 2.9 40.5 + - + +
128A LEU* 3.6 22.7 - - + -
137A ASP* 4.4 2.0 - - - +
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Residues in contact with ALA 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 GLY 3.1 11.2 + - - +
61A GLU* 3.5 12.6 - - - +
62A ALA 3.2 0.2 - - - -
63A ALA* 1.3 76.3 - - - +
65A ARG* 1.3 52.8 + - - +
67A HIS* 3.7 1.0 - - - +
68A PHE* 2.7 37.7 + - - +
103A TRP* 5.5 2.7 - - + +
104A VAL 5.4 1.6 - - - -
105A LEU* 3.8 31.4 - - + +
126A GLN* 5.0 5.0 + - + -
128A LEU* 3.5 24.0 - - + +
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Residues in contact with ARG 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* 3.0 50.0 + - - +
62A ALA* 4.0 6.7 - - - +
64A ALA* 1.3 77.3 - - - +
66A TYR* 1.3 66.9 + - - +
68A PHE* 3.2 7.7 + - + +
69A GLU* 3.0 30.0 + - + +
82A VAL* 5.2 14.1 - - + +
85A VAL* 3.6 25.1 - - - +
105A LEU* 3.1 30.0 - - + +
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Residues in contact with TYR 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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55A GLN* 4.8 19.5 - - + +
58A VAL* 3.3 41.5 - - + -
62A ALA 2.9 19.9 + - - +
63A ALA 3.7 0.9 - - - +
65A ARG* 1.3 79.4 - - - +
67A HIS* 1.3 81.2 + + - +
69A GLU* 3.6 6.2 + - - +
70A ASP* 3.6 15.7 + - + +
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Residues in contact with HIS 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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52A LEU* 3.6 29.6 - - + +
53A GLU 6.2 0.4 - - - -
55A GLN* 6.4 1.8 - - + -
58A VAL* 5.3 2.0 + - - +
63A ALA* 2.9 30.8 + - + +
64A ALA 4.0 1.6 - - - +
66A TYR* 1.3 91.0 - + - +
68A PHE* 1.3 65.9 + - - +
70A ASP* 3.0 20.0 + - - +
71A VAL* 3.0 20.7 + - + +
126A GLN* 5.5 1.1 - - - +
128A LEU* 3.8 11.9 - - + +
137A ASP* 4.6 14.1 + - - +
139A LEU* 3.5 37.2 - - + +
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Residues in contact with PHE 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 ALA 2.7 23.0 + - - +
65A ARG* 3.4 11.4 - - + +
67A HIS* 1.3 72.7 - - - +
69A GLU* 1.3 62.7 + - + +
71A VAL* 3.0 3.6 + - + +
72A GLY* 2.7 39.6 + - - -
80A VAL* 3.2 45.1 - - + -
81A HIS 5.2 1.3 - - - -
82A VAL* 6.4 1.3 - - + -
105A LEU* 3.6 22.9 - - + -
107A GLY* 5.1 9.4 - - - -
109A GLN* 3.3 19.1 - - - -
124A LEU* 5.2 4.5 - - + -
126A GLN* 3.1 44.2 - - - +
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Residues in contact with GLU 69 (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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65A ARG* 3.0 19.3 + - + +
66A TYR* 3.9 7.0 - - - +
67A HIS 3.3 0.2 - - - -
68A PHE* 1.3 82.4 - - + +
70A ASP* 1.3 57.2 + - - +
72A GLY 5.0 1.0 - - - -
73A GLY* 2.9 35.1 + - - +
74A VAL* 3.6 2.3 + - - +
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Residues in contact with ASP 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 TYR* 3.6 9.7 + - + +
67A HIS* 3.0 18.0 + - - +
69A GLU* 1.3 78.9 - - - +
71A VAL* 1.3 61.2 + - + +
74A VAL* 2.9 42.0 - - - +
75A GLN* 3.9 4.9 + - - -
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Residues in contact with VAL 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 HIS* 3.1 18.2 - - + +
68A PHE* 3.0 6.8 + - - +
70A ASP* 1.3 78.9 - - + +
72A GLY* 1.3 59.5 - - - +
73A GLY 3.1 7.4 + - - -
75A GLN* 3.5 37.6 + - - +
124A LEU* 5.1 15.0 - - + -
126A GLN* 5.2 8.7 - - - +
139A LEU* 4.8 17.3 - - + -
141A THR* 5.9 6.1 - - + -
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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 PHE* 2.7 26.4 + - - -
69A GLU* 4.0 2.2 - - - -
71A VAL* 1.3 74.0 - - - +
73A GLY* 1.3 54.0 + - - -
75A GLN 4.6 0.2 - - - -
76A GLY 3.2 1.1 - - - +
77A ALA* 2.9 43.6 - - - +
80A VAL* 5.5 4.9 - - - +
109A GLN* 4.7 12.7 - - - +
124A LEU* 6.4 0.4 - - - -
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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