Contacts of the helix formed by residues 61 - 73 (chain D) in PDB entry 5GQQ
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 61 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D PRO 3.2 0.8 + - - -
60D PHE* 1.3 70.7 - - - +
62D PRO* 1.4 67.7 - - - +
63D VAL* 2.8 25.4 + - - +
64D THR* 3.1 23.8 + - - +
65D VAL* 3.0 24.6 + - - +
138D PHE 5.5 0.8 + - - -
140D ARG* 3.5 25.1 - - - +
149D ASP* 2.9 23.7 + - + +
150D ASP* 3.1 20.4 + - - +
153D GLN* 3.8 14.1 - - - +
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Residues in contact with PRO 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ASP* 6.1 1.8 - - - -
66C ARG* 4.1 31.6 - - + +
45D ASP* 4.7 1.6 - - - +
49D GLN* 3.9 17.7 - - - +
59D PRO* 5.0 1.3 - - + +
60D PHE 3.0 8.9 - - - +
61D ASN* 1.4 86.1 - - - +
63D VAL* 1.3 62.7 + - + +
65D VAL* 3.7 8.6 - - + +
66D ARG* 3.0 28.9 + - - +
140D ARG* 4.1 11.2 - - - +
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 4.4 22.2 - - + -
191C VAL 5.2 9.9 - - - +
61D ASN* 2.8 18.1 + - - +
62D PRO* 1.3 74.6 - - + +
64D THR* 1.3 57.2 + - - +
66D ARG* 3.3 7.6 + - + +
67D SER* 2.9 34.5 + - - +
153D GLN* 3.7 26.7 - - + +
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 3.8 18.6 - - + -
61D ASN* 3.1 18.6 + - - -
63D VAL* 1.3 78.6 - - - +
65D VAL* 1.3 62.8 + - - +
67D SER* 3.0 3.3 + - - -
68D ILE* 2.9 30.9 + - + +
149D ASP 3.1 23.7 + - - +
152D ILE* 3.9 25.4 - - + -
153D GLN* 3.1 30.2 - - - +
156D ILE* 5.6 1.1 - - + -
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASP* 3.5 39.0 - - + +
48D LEU* 4.0 16.4 - - + -
49D GLN* 4.0 24.0 - - + -
52D LEU* 4.3 6.7 - - + -
60D PHE* 3.6 23.6 - - + +
61D ASN 3.0 18.3 + - - +
62D PRO* 3.7 9.2 - - + +
63D VAL 3.3 0.2 - - - -
64D THR* 1.3 77.0 - - - +
66D ARG* 1.3 57.1 + - - +
68D ILE* 3.3 8.9 + - - +
69D ILE* 2.9 29.2 + - + +
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Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 3.8 33.9 - - - +
63C VAL* 4.8 16.6 - - + +
45D ASP* 3.2 39.9 + - - +
62D PRO 3.0 17.3 + - - +
63D VAL* 3.5 8.1 - - + +
65D VAL* 1.3 77.4 - - - +
67D SER* 1.3 64.0 + - - +
69D ILE* 3.8 14.6 - - - +
70D SER* 3.0 38.5 + - - +
78D ALA* 4.5 16.2 - - - +
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Residues in contact with SER 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D VAL* 2.9 19.7 + - - +
64D THR 3.0 8.5 + - - -
66D ARG* 1.3 76.6 - - - +
68D ILE* 1.3 66.4 + - - +
70D SER* 3.3 8.9 + - - -
71D MET* 3.0 27.1 + - - +
153D GLN* 3.4 18.4 + - - -
156D ILE* 4.3 16.2 - - - +
160D ARG* 4.7 17.6 + - - +
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Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 4.5 4.9 - - + -
52D LEU* 4.9 5.4 - - + -
60D PHE* 4.9 2.5 - - + -
64D THR* 2.9 35.2 + - + +
65D VAL* 3.7 9.6 - - - +
67D SER* 1.3 73.5 - - - +
69D ILE* 1.3 67.7 + - - +
71D MET* 2.9 25.5 + - + +
72D PHE* 3.3 16.0 + - + -
88D VAL* 3.7 33.0 - - + -
91D TYR* 4.1 19.7 - - + -
92D ILE* 3.7 31.2 - - + -
152D ILE* 5.0 7.2 - - + -
156D ILE* 5.4 0.7 - - + -
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Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE 3.9 20.2 - - - +
45D ASP* 3.7 26.5 - - - +
48D LEU* 3.7 26.9 - - + -
65D VAL* 2.9 21.7 + - + +
66D ARG* 3.8 17.5 - - - +
68D ILE* 1.3 75.8 - - - +
70D SER* 1.3 58.1 + - - +
72D PHE* 3.1 1.9 + - - -
73D ASP* 2.7 32.9 + - + +
78D ALA* 4.0 0.7 - - - -
79D GLY* 3.8 28.0 - - - +
80D VAL* 4.0 20.9 - - + +
88D VAL* 5.5 0.4 - - + -
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Residues in contact with SER 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ARG* 3.0 35.9 + - - +
67D SER* 3.3 12.0 + - - -
69D ILE* 1.3 78.7 - - - +
71D MET* 1.3 62.5 + - - +
72D PHE 3.6 0.2 + - - -
73D ASP* 4.1 14.6 - - - +
160D ARG* 5.4 4.0 + - - -
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Residues in contact with MET 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D SER 3.0 18.6 + - - +
68D ILE* 2.9 13.9 + - - +
70D SER* 1.3 81.9 - - - +
72D PHE* 1.3 72.4 + - + +
73D ASP 5.1 0.6 - - - +
91D TYR* 3.4 51.8 - - + +
156D ILE* 3.8 18.6 - - + -
160D ARG* 4.2 15.9 - - - +
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Residues in contact with PHE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ILE* 3.4 14.6 - - + -
69D ILE 3.1 2.0 + - - -
71D MET* 1.3 99.3 - - + +
73D ASP* 1.3 62.3 + - - +
74D ARG* 3.2 12.2 + - - +
80D VAL* 4.1 5.4 - - + -
84D GLU* 3.5 25.7 - - + +
87D GLY* 3.7 25.1 - - - -
88D VAL* 3.6 27.6 - - + -
91D TYR* 3.5 48.7 - + + -
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Residues in contact with ASP 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ILE* 2.7 25.9 + - + +
70D SER* 4.1 13.3 - - - +
71D MET 3.7 0.5 - - - +
72D PHE* 1.3 69.4 - - - +
74D ARG* 1.3 60.4 + - - +
75D GLU 2.8 23.4 + - - -
76D ASN* 3.4 8.4 + - - -
77D LYS* 2.7 39.4 + - - -
78D ALA* 3.0 12.6 + - - -
79D GLY 3.0 26.3 + - - +
80D VAL* 3.9 1.0 - - - +
84D GLU* 3.8 4.7 - - - -
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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