Contacts of the helix formed by residues 65 - 80 (chain D) in PDB entry 3QS7
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 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C SER 4.0 9.0 - - - -
24C ASP* 3.3 18.6 - - - -
26C LEU 3.4 11.7 + - - -
28C GLN* 4.0 4.7 + - - -
64D ALA* 1.3 75.8 - - - +
66D SER* 1.3 66.4 + - - -
67D LYS 3.2 2.9 - - - -
68D MET* 2.9 5.5 + - - +
69D GLN* 2.8 22.4 + - - +
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Residues in contact with SER 66 (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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24C ASP* 3.3 29.5 + - - +
64D ALA 3.9 0.4 + - - -
65D GLY* 1.3 71.1 - - - +
67D LYS* 1.3 68.3 + - - +
69D GLN* 3.5 15.8 - - - +
70D GLY* 3.8 4.3 + - - -
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Residues in contact with LYS 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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24C ASP* 3.0 14.3 + - + +
25C TYR* 3.1 42.9 - - + +
66D SER* 1.3 77.8 + - - +
68D MET* 1.3 64.1 + - - +
69D GLN 3.2 1.8 - - - -
70D GLY* 3.3 9.9 + - - -
71D LEU* 3.6 15.4 + - - +
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Residues in contact with MET 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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24C ASP 3.1 4.0 + - - -
25C TYR* 3.7 30.0 - - - +
27C LEU* 4.5 11.0 - - + -
22D LEU* 3.5 25.8 - - + -
25D TYR* 3.3 43.1 - - + +
26D LEU* 3.7 19.3 - - + -
64D ALA* 3.7 15.3 - - + -
65D GLY 2.9 14.6 + - - +
67D LYS* 1.3 73.7 - - - +
69D GLN* 1.3 64.4 + - - +
71D LEU* 3.2 6.0 + - + +
72D LEU* 3.0 29.6 + - + +
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Residues in contact with GLN 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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61D LYS* 4.6 13.9 - - + +
64D ALA* 3.9 13.6 - - + +
65D GLY 2.8 17.1 + - - +
66D SER* 3.5 11.0 - - - +
67D LYS 3.2 0.2 - - - -
68D MET* 1.3 77.8 - - - +
70D GLY* 1.3 56.5 + - - +
72D LEU* 3.5 4.5 + - - +
73D GLU* 2.9 32.7 + - - +
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Residues in contact with GLY 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 SER 3.8 3.5 + - - -
67D LYS* 3.3 9.4 + - - -
68D MET 3.2 0.8 - - - -
69D GLN* 1.3 78.0 - - - +
71D LEU* 1.3 58.2 + - - +
73D GLU* 3.8 4.1 - - - +
74D ARG* 2.9 41.9 + - - +
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Residues in contact with LEU 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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25C TYR* 4.1 15.0 - - + -
18D LYS 4.7 1.1 - - - +
21D GLU* 4.1 24.7 - - + +
22D LEU* 3.8 17.2 - - + +
25D TYR* 3.5 44.9 - - + -
67D LYS 3.8 7.9 - - - +
68D MET* 3.2 16.0 + - + +
70D GLY* 1.3 74.5 - - - +
72D LEU* 1.3 65.7 + - - +
74D ARG* 3.5 16.7 + - - +
75D VAL* 3.2 28.2 + - - +
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Residues in contact with LEU 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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27C LEU* 4.9 2.7 - - + -
22D LEU* 3.7 26.2 - - + -
26D LEU* 5.3 1.8 - - + -
57D MET* 4.3 18.8 - - - +
60D LEU* 3.4 61.2 - - + +
61D LYS* 3.5 6.3 - - + +
64D ALA* 3.5 20.4 - - + -
68D MET* 3.0 22.6 + - + +
69D GLN* 3.8 3.8 - - - +
71D LEU* 1.3 73.9 - - - +
73D GLU* 1.3 53.5 + - - +
75D VAL* 2.9 7.6 + - - +
76D ASN* 2.7 36.2 + - - +
101D ILE* 5.3 2.2 - - + -
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Residues in contact with GLU 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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61D LYS* 5.6 0.6 - - - +
69D GLN 2.9 18.9 + - - +
70D GLY* 3.8 5.6 - - - +
72D LEU* 1.3 77.5 - - - +
74D ARG* 1.3 58.1 + - + +
76D ASN* 3.0 26.3 + - - +
77D THR* 2.8 57.7 + - + +
307H ARG* 3.3 21.6 + - - +
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Residues in contact with ARG 74 (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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18D LYS* 4.1 24.6 + - + +
21D GLU* 3.4 24.4 + - - +
70D GLY* 2.9 29.9 + - - +
71D LEU* 3.8 17.5 - - - +
72D LEU 3.2 0.2 - - - -
73D GLU* 1.3 77.9 - - + +
75D VAL* 1.3 59.6 + - + +
77D THR* 2.7 23.5 + - + -
78D GLU* 3.8 4.5 + - - +
303H TYR 5.7 2.8 + - - -
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Residues in contact with VAL 75 (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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18D LYS* 3.1 35.9 - - + +
19D ILE* 4.1 20.2 - - + -
22D LEU* 3.8 19.5 - - + -
57D MET* 3.7 27.8 - - + -
71D LEU 3.2 12.2 + - - +
72D LEU 2.9 7.2 + - - +
74D ARG* 1.3 76.1 - - - +
76D ASN* 1.3 65.7 + - - +
77D THR 3.2 0.4 - - - -
78D GLU* 3.3 18.6 + - + +
79D ILE* 3.6 12.1 - - + +
105D LEU* 4.9 2.5 - - + -
108D THR* 5.4 4.0 - - + -
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Residues in contact with ASN 76 (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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54D GLN* 2.9 27.2 + - - +
57D MET* 3.6 25.5 + - + +
58D GLU* 3.3 24.5 + - - +
72D LEU 2.7 13.4 + - - +
73D GLU* 3.1 33.4 + - - +
75D VAL* 1.3 78.3 - - - +
77D THR* 1.3 48.9 + - - +
79D ILE* 3.1 7.8 + - - +
80D HIS* 2.8 36.0 + - - +
307H ARG* 3.6 13.7 - - - +
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Residues in contact with THR 77 (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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73D GLU* 2.8 37.5 + - + +
74D ARG* 2.7 27.4 + - + +
76D ASN* 1.3 75.8 - - - +
78D GLU* 1.3 60.1 + - - +
79D ILE 3.3 1.0 + - - -
80D HIS* 3.6 15.6 + - - +
81D PHE 4.8 1.4 + - - -
303H TYR* 3.8 41.2 + - + +
305H THR 5.4 3.4 - - - +
307H ARG* 3.7 29.9 - - + +
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Residues in contact with GLU 78 (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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10D PRO 4.1 6.0 - - - +
11D ILE* 4.9 2.3 - - - -
12D SER* 4.8 4.3 + - - +
15D PHE* 4.1 29.1 - - + +
18D LYS* 5.5 2.7 - - + -
19D ILE* 6.0 2.0 - - + -
74D ARG 4.3 7.2 - - - +
75D VAL* 3.3 14.7 + - + +
76D ASN 3.3 0.8 - - - -
77D THR* 1.3 80.3 + - - +
79D ILE* 1.4 64.7 + - + +
80D HIS 3.8 0.2 - - - -
81D PHE* 3.4 18.3 - - - -
112D LEU* 4.1 7.7 - - + +
303H TYR* 4.5 12.1 - - + -
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Residues in contact with ILE 79 (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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50D LEU* 3.8 24.9 - - + +
53D ALA* 4.1 8.3 - - + -
54D GLN* 3.5 39.5 - - + +
57D MET* 4.0 16.6 - - + -
75D VAL* 3.6 11.9 - - + +
76D ASN* 3.5 11.2 - - - +
78D GLU* 1.4 82.8 - - + +
80D HIS* 1.3 64.4 + - - +
81D PHE* 3.2 11.9 + - + -
82D VAL* 3.3 24.1 + - - +
108D THR* 4.0 11.7 - - + -
112D LEU* 3.7 27.4 - - + -
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Residues in contact with HIS 80 (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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54D GLN* 3.3 25.7 + - - -
58D GLU* 3.9 13.1 + - - -
76D ASN* 2.8 15.1 + - - +
77D THR 3.6 9.8 + - - +
79D ILE* 1.3 74.0 - - - +
81D PHE* 1.3 61.7 + - - +
82D VAL* 3.0 5.0 + - - -
83D THR* 2.6 47.5 + - + -
307H ARG* 3.2 54.5 + - - +
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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