Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 1G8I
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 5.0 2.2 - - - +
52A TYR* 4.0 18.4 - - + +
53A LYS* 3.7 43.3 - - + +
56A PHE* 3.7 12.1 - - + +
59A GLY 2.9 24.0 - - - +
60A ASP* 1.4 74.5 - - - +
62A THR* 1.3 57.3 + - - +
63A LYS 3.4 1.1 - - - -
64A PHE 3.3 2.1 + - - +
65A ALA* 2.8 34.1 + - - +
131A MET* 4.0 30.1 - - + +
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Residues in contact with THR 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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49A GLN* 2.8 44.9 + - - +
53A LYS* 5.5 4.2 - - - +
60A ASP* 2.8 28.9 + - - -
61A PRO* 1.3 78.1 - - - +
63A LYS* 1.3 66.4 + - - +
66A THR* 3.1 20.4 + - - +
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Residues in contact with LYS 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 ASP* 4.2 5.6 + - - +
61A PRO 3.4 0.4 - - - -
62A THR* 1.3 81.9 - - - +
64A PHE* 1.3 62.5 + - - +
66A THR* 3.3 7.3 + - + -
67A PHE* 3.1 49.7 + - + -
123A ASP* 2.8 40.9 + - - +
126A ASP* 3.9 16.5 + - - -
127A ALA* 3.8 16.0 - - + +
130A GLN* 4.4 15.3 - - + +
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Residues in contact with PHE 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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52A TYR* 3.9 17.5 - + - -
60A ASP 5.3 0.2 + - - -
61A PRO 3.3 4.2 + - - +
63A LYS* 1.3 76.2 - - - +
65A ALA* 1.3 66.2 + - - +
67A PHE* 3.1 8.3 + + + +
68A VAL* 3.0 48.0 + - + +
107A LEU* 4.3 11.2 - - + -
124A ILE* 4.2 16.6 - - + -
127A ALA* 3.7 26.7 + - + +
128A ILE* 3.7 31.9 - - + -
131A MET* 3.4 40.6 - - + -
952A 1PE 4.1 22.9 - - - -
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Residues in contact with ALA 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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48A PHE* 3.4 6.2 - - + -
49A GLN* 3.5 26.0 - - + +
52A TYR* 3.5 42.6 - - + -
61A PRO 2.8 23.0 + - - +
64A PHE* 1.3 73.4 - - - +
66A THR* 1.3 57.7 + - - +
68A VAL 3.3 0.3 + - - -
69A PHE* 2.8 30.5 + - - +
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Residues in contact with THR 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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45A ALA* 5.7 4.6 - - - +
49A GLN* 3.7 12.1 + - - -
62A THR* 3.1 21.8 + - - +
63A LYS* 3.5 8.3 - - + +
65A ALA* 1.3 76.9 - - - +
67A PHE* 1.3 70.4 + - + +
69A PHE* 3.7 7.4 - - + +
70A ASN* 3.1 39.6 + - - +
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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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63A LYS* 3.1 47.1 + - + -
64A PHE* 3.1 11.3 + + + +
66A THR* 1.3 85.4 - - + +
68A VAL* 1.3 62.4 + - - +
70A ASN* 3.5 16.6 + - - +
71A VAL* 3.6 7.4 + - - +
107A LEU* 3.5 16.5 - - + +
110A LEU* 4.0 24.9 - - + -
123A ASP* 3.6 34.8 - - + -
124A ILE* 3.5 28.9 - - + -
127A ALA* 3.8 11.4 - - + -
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Residues in contact with VAL 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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48A PHE* 3.8 10.3 - - + -
52A TYR* 3.7 19.1 - - + +
64A PHE* 3.0 53.8 + - + +
65A ALA 3.8 3.4 - - - +
67A PHE* 1.3 75.1 - - - +
69A PHE* 1.3 67.8 + - - +
71A VAL* 2.9 22.9 - - - +
72A PHE* 3.0 32.6 + - + -
103A TRP* 4.2 10.8 - - + -
107A LEU* 4.1 14.8 - - + -
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Residues in contact with PHE 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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43A LEU 3.6 5.4 - - - -
44A ASP 3.5 6.5 - - - -
45A ALA* 3.3 34.3 - - + +
48A PHE* 3.4 35.2 - - + -
49A GLN* 5.8 0.4 - - - +
65A ALA 2.8 18.4 + - - +
66A THR* 3.7 9.0 - - + +
67A PHE 3.3 0.2 - - - -
68A VAL* 1.3 77.7 - - - +
70A ASN* 1.3 71.2 + - - +
72A PHE* 3.1 5.7 + - - +
73A ASP* 2.9 43.1 + - + +
78A GLY* 3.5 31.4 - - - -
79A ARG* 4.0 3.8 - - - -
80A ILE* 3.5 22.2 - - + -
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Residues in contact with ASN 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 THR* 3.1 29.8 + - - +
67A PHE* 3.8 12.1 - - - +
68A VAL 3.2 0.2 - - - -
69A PHE* 1.3 94.7 - - - +
71A VAL* 1.3 58.4 + - - +
73A ASP* 3.4 9.3 - - - +
76A LYS* 2.8 41.0 + - - +
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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 PHE 3.6 6.8 + - - +
68A VAL* 2.9 25.8 + - - +
70A ASN* 1.3 77.0 - - - +
72A PHE* 1.3 67.4 + - + +
73A ASP 3.2 0.6 + - - -
74A GLU* 4.0 9.5 + - - +
76A LYS* 4.7 2.8 + - - +
88A ALA* 5.5 0.3 - - - +
103A TRP* 2.9 57.8 + - + +
106A LYS* 4.1 31.4 - - + +
107A LEU* 4.5 10.8 - - + +
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Residues in contact with PHE 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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48A PHE* 4.3 9.6 - + - -
68A VAL* 3.0 39.1 + - + +
69A PHE 3.5 3.4 - - - +
71A VAL* 1.3 88.2 - - + +
73A ASP* 1.3 52.6 + - - +
74A GLU* 2.8 16.1 + - - +
80A ILE* 3.4 30.3 - - + -
84A GLU* 3.2 24.4 - - - +
85A PHE* 4.1 33.9 - + - -
88A ALA* 3.5 37.2 - - + +
89A LEU* 4.3 16.2 - - + -
92A THR* 5.0 5.4 - - + -
103A TRP* 3.8 11.2 - + - -
954A P6G 4.5 13.0 - - - -
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Residues in contact with ASP 73 (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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69A PHE* 2.9 28.8 + - + +
70A ASN* 3.7 10.2 - - - +
71A VAL 3.2 0.4 - - - -
72A PHE* 1.3 72.4 - - - +
74A GLU* 1.3 65.2 + - - +
75A ASN* 2.7 8.6 - - - +
76A LYS* 3.0 45.5 + - - -
77A ASP* 3.0 2.9 - - - +
78A GLY* 3.0 19.7 + - - -
79A ARG 2.9 6.9 - - - +
80A ILE* 4.2 4.7 - - + +
84A GLU* 4.0 4.9 - - - -
1597A CA 2.2 32.7 - - - -
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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