Contacts of the helix formed by residues 65 - 77 (chain D) in PDB entry 6S1M
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 THR 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D CYS* 5.5 0.9 - - - +
64D ILE* 1.3 93.4 - - - +
66D ARG* 1.3 66.6 + - - +
67D LEU* 4.4 9.0 - - + +
68D GLN* 2.8 27.9 + - - -
69D ARG* 3.9 9.2 + - - +
98D GLN* 3.5 29.4 - - + +
99D CYS* 5.1 2.2 - - - +
100D SER* 5.2 5.3 - - - +
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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
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46D LEU* 5.9 0.8 - - - +
49D LEU* 3.5 37.8 + - - +
50D ARG 5.2 0.2 - - - +
52D PHE* 4.2 17.1 - - + -
53D ASP* 2.3 39.0 + - - +
65D THR* 1.3 77.8 - - - +
67D LEU* 1.3 60.1 + - - +
68D GLN 3.3 0.2 - - - -
69D ARG* 3.4 7.5 + - - +
70D TRP* 3.0 25.1 + - - +
84D VAL* 5.3 0.4 - - + -
88D LEU* 3.7 25.6 - - + -
96D ARG 4.4 4.0 + - - -
97D PHE* 2.4 40.7 + - - +
98D GLN* 4.6 4.4 + - - -
99D CYS* 2.8 34.4 + - - +
100D SER* 4.0 2.3 - - - +
101D LEU* 4.1 7.5 - - - +
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Residues in contact with LEU 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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65D THR* 4.4 6.0 - - + +
66D ARG* 1.3 76.9 - - - +
68D GLN* 1.3 62.0 + - + +
70D TRP* 3.3 8.3 + - + +
71D CYS* 3.0 42.1 + - - -
85D TRP* 5.2 15.5 - - + +
88D LEU* 4.2 37.4 - - + +
98D GLN* 5.6 8.9 - - + +
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Residues in contact with GLN 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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48B ARG* 5.6 3.1 + - - +
388B TYR* 2.9 39.8 + - + +
64D ILE* 4.0 7.9 - - + +
65D THR* 2.8 40.9 + - - +
66D ARG 3.3 0.6 - - - -
67D LEU* 1.3 81.6 - - + +
69D ARG* 1.3 58.3 + - - +
71D CYS* 3.4 5.2 + - - +
72D ARG* 2.9 29.0 + - - +
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Residues in contact with ARG 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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52D PHE* 2.6 52.1 + - + -
53D ASP* 4.1 18.8 + - - +
55D ALA 3.3 21.6 + - - -
58D TYR* 3.4 27.9 - - + +
59D GLY 3.0 24.4 + - - -
61D CYS* 3.4 33.1 + - + +
64D ILE* 4.1 15.6 - - + +
65D THR 3.9 12.9 + - - +
66D ARG* 3.4 8.4 + - - +
67D LEU 3.3 0.2 - - - -
68D GLN* 1.3 74.3 - - - +
70D TRP* 1.3 63.7 - - - +
72D ARG* 3.7 8.9 + - - +
73D ALA* 3.1 24.4 + - - +
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Residues in contact with TRP 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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52D PHE* 3.9 29.1 - + + -
66D ARG 3.0 14.7 + - - +
67D LEU* 3.6 13.0 - - + +
68D GLN 3.3 0.2 - - - -
69D ARG* 1.3 78.7 - - - +
71D CYS* 1.3 77.3 + - - +
73D ALA* 3.7 3.8 + - - +
74D LYS* 3.3 45.9 + - + +
80D PRO* 3.5 27.2 - - + +
81D PRO* 3.5 24.1 + - - +
82D PRO* 5.0 3.1 - - + -
84D VAL* 4.4 17.0 - - + -
85D TRP* 3.9 44.4 - + + +
88D LEU* 5.5 4.3 - - + -
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Residues in contact with CYS 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 LEU* 3.0 36.2 + - - +
68D GLN* 4.0 4.7 - - - +
70D TRP* 1.3 92.1 - - - +
72D ARG* 1.3 60.9 + - - +
74D LYS* 3.7 4.6 - - - +
75D GLN* 3.0 29.6 + - - +
85D TRP* 6.1 1.1 - - - -
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Residues in contact with ARG 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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52B HIS* 3.2 26.0 + - - +
55B ALA* 6.2 0.2 - - - -
56B THR* 4.3 10.6 + - - -
388B TYR* 3.2 39.5 + - + -
389B LYS* 4.5 17.9 - - + +
58D TYR 3.7 7.2 + - - -
59D GLY* 3.6 9.0 - - - -
60D PRO* 3.5 16.6 - - - +
61D CYS* 2.8 37.3 - - - -
64D ILE* 4.6 4.0 - - - -
68D GLN 2.9 17.4 + - - +
69D ARG* 3.3 7.2 + - - +
71D CYS* 1.3 78.6 - - - +
73D ALA* 1.3 61.1 + - - +
75D GLN* 3.5 5.7 + - - +
76D MET* 3.3 41.0 + - + +
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Residues in contact with ALA 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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52D PHE* 6.1 1.6 - - + -
58D TYR* 4.4 27.1 - - + +
69D ARG 3.1 15.6 + - - +
70D TRP* 4.1 4.3 - - - +
72D ARG* 1.3 77.3 - - - +
74D LYS* 1.3 51.7 + - - +
76D MET* 3.5 10.2 - - - -
77D GLY 2.6 27.5 + - - -
78D LEU* 3.0 28.6 + - + -
80D PRO* 4.3 12.8 - - + -
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Residues in contact with LYS 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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70D TRP* 3.3 40.0 + - + +
71D CYS* 3.7 8.3 - - - +
72D ARG 3.3 0.8 - - - -
73D ALA* 1.3 75.9 - - - +
75D GLN* 1.3 64.5 + - - +
77D GLY* 3.0 14.1 + - - +
79D GLU* 5.9 0.6 + - - -
80D PRO* 3.5 28.8 + - + +
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Residues in contact with GLN 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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389B LYS 5.6 1.4 - - - +
390B THR* 5.0 11.7 + - - +
71D CYS 3.0 17.0 + - - +
72D ARG* 3.7 6.5 - - - +
74D LYS* 1.3 77.8 - - - +
76D MET* 1.3 77.6 + - - +
77D GLY* 4.3 0.3 - - - -
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Residues in contact with MET 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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56B THR* 4.2 24.2 - - - +
59B ILE* 3.7 31.2 - - + -
60B GLN* 5.8 1.6 - - - -
389B LYS 5.1 2.5 - - - +
58D TYR 5.5 1.8 - - - +
72D ARG* 3.3 43.4 + - + +
73D ALA* 4.1 2.2 - - - +
75D GLN* 1.3 89.8 - - - +
77D GLY* 1.3 64.0 + - - +
78D LEU* 3.4 30.6 + - + +
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Residues in contact with GLY 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 ALA 2.6 10.8 + - - -
74D LYS* 3.0 19.5 + - - -
75D GLN 3.0 0.6 - - - -
76D MET* 1.3 79.2 - - - +
78D LEU* 1.3 65.2 - - - +
79D GLU* 3.4 4.8 + - - +
80D PRO* 4.5 3.4 - - - -
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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