Contacts of the helix formed by residues 69 - 84 (chain D) in PDB entry 3P9K
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 GLU 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C GLY 5.7 3.7 + - - -
323C GLY* 6.0 2.4 - - - -
67D ASN* 2.9 20.2 + - - +
68D PRO* 1.3 79.3 - - + +
70D ALA* 1.3 64.2 + - - +
71D PRO* 3.3 3.8 - - - -
72D ASP* 3.0 16.2 + - + +
73D MET* 3.0 29.4 + - + +
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Residues in contact with ALA 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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144C VAL* 3.8 23.6 - - + +
59D ALA* 4.2 12.8 - - + -
62D LEU* 5.3 0.7 - - + -
65D ALA* 4.7 12.8 - - + -
67D ASN* 3.0 24.4 + - + +
69D GLU* 1.3 76.9 - - - +
71D PRO* 1.3 62.6 - - + +
73D MET* 3.2 6.0 + - - +
74D VAL* 2.8 36.4 + - + +
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Residues in contact with PRO 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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55D PRO* 3.2 23.8 - - + +
56D THR* 4.0 34.1 - - + +
59D ALA* 3.9 13.7 - - + -
67D ASN 4.2 0.9 - - - +
68D PRO 3.4 14.6 - - - +
69D GLU 3.3 5.2 - - - -
70D ALA* 1.3 94.9 - - + +
72D ASP* 1.3 56.3 + - - +
74D VAL* 3.5 1.2 + - + +
75D ASP* 2.9 22.9 + - - +
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Residues in contact with ASP 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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325C ARG* 2.8 44.8 + - - -
69D GLU* 3.0 19.5 + - + +
71D PRO* 1.3 76.5 - - - +
73D MET* 1.3 68.6 + - - +
75D ASP* 3.2 11.0 + - - +
76D ARG* 3.1 32.4 + - - +
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Residues in contact with MET 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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140C LEU* 4.6 2.7 - - + -
143C ALA* 3.7 34.1 - - + +
144C VAL* 3.8 22.4 - - + +
148C GLY 4.2 10.1 - - - +
150C PRO* 5.1 1.8 - - + -
318C LEU* 3.6 38.8 - - + +
67D ASN* 3.4 28.3 - - - -
69D GLU* 3.0 22.5 + - + +
70D ALA* 3.6 6.1 - - - +
72D ASP* 1.3 77.4 - - + +
74D VAL* 1.3 62.4 + - - +
76D ARG* 3.3 7.2 + - - +
77D ILE* 3.0 29.2 + - - +
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C VAL* 4.4 10.5 - - + -
41D LEU* 4.3 14.1 - - + -
55D PRO* 4.2 8.7 - - + +
58D VAL* 4.0 21.5 - - + -
59D ALA* 4.6 5.2 - - + -
62D LEU* 4.3 24.5 - - + -
70D ALA 2.8 26.0 + - - +
71D PRO* 3.7 5.8 - - + +
73D MET* 1.3 74.0 - - - +
75D ASP* 1.3 56.9 + - - +
77D ILE* 3.3 8.7 + - + +
78D LEU* 2.9 50.3 + - + +
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Residues in contact with ASP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D PRO* 3.5 22.5 - - + +
71D PRO 2.9 18.0 + - - +
72D ASP* 3.2 13.7 + - - +
74D VAL* 1.3 75.0 - - - +
76D ARG* 1.3 62.0 + - - +
78D LEU 3.5 0.2 + - - -
79D ARG* 2.9 29.3 + - - +
101D ARG* 2.9 36.1 + - - +
103D TYR* 2.6 37.0 + - - -
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Residues in contact with ARG 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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311C PHE* 5.9 0.2 - - - +
314C ASP* 3.0 61.6 + - - +
315C MET* 3.7 12.6 - - - +
318C LEU* 3.4 30.2 - - + +
323C GLY* 4.9 2.6 + - - -
324C GLY 2.9 28.8 + - - -
325C ARG* 3.3 29.1 - - - +
72D ASP* 3.1 33.1 + - - +
73D MET* 3.3 8.9 + - - +
75D ASP* 1.3 74.5 - - + +
77D ILE* 1.3 66.1 + - - +
79D ARG* 3.4 18.9 + - - +
80D LEU* 3.2 22.2 + - - +
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Residues in contact with ILE 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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140C LEU* 4.3 17.0 - - + -
144C VAL* 4.1 26.0 - - + -
315C MET* 3.9 25.1 - - + -
318C LEU* 4.3 2.7 - - + -
32D THR* 3.7 17.1 - - + +
35D ASN* 5.5 2.0 - - + -
36D ALA* 4.3 4.7 - - + -
39D LEU* 4.4 12.6 - - + -
41D LEU* 3.9 20.4 - - + -
73D MET 3.0 23.5 + - - +
74D VAL* 3.5 7.6 - - - +
76D ARG* 1.3 77.9 - - - +
78D LEU* 1.3 62.3 + - - +
80D LEU* 3.3 3.6 + - - +
81D LEU* 3.1 31.6 + - + +
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Residues in contact with LEU 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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41D LEU* 4.1 22.2 - - + -
42D LEU* 5.1 0.7 - - + -
45D LEU* 4.4 20.9 - - + -
58D VAL* 4.5 16.2 - - + -
74D VAL* 2.9 36.9 + - + +
77D ILE* 1.3 73.7 - - - +
79D ARG* 1.3 60.7 + - - +
81D LEU* 3.7 17.4 - - + -
82D ALA* 2.8 31.4 + - - +
87D VAL* 3.8 9.3 - - + +
103D TYR* 3.6 46.9 - - + -
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Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU* 3.4 26.2 - - - +
311C PHE* 3.6 36.6 - - + -
314C ASP* 3.0 35.4 + - - -
325C ARG* 5.3 4.2 - - - +
326C GLU 5.1 0.6 + - - -
328C TYR* 2.9 33.5 + - - -
75D ASP* 2.9 18.8 + - - +
76D ARG* 3.7 21.5 + - - +
77D ILE 3.3 0.2 - - - -
78D LEU* 1.3 76.2 - - - +
80D LEU* 1.3 62.6 + - - +
82D ALA* 3.5 3.7 + - - +
83D SER* 3.2 20.8 + - - -
89D CYS* 5.7 3.4 - - - -
101D ARG* 3.8 23.3 - - - +
103D TYR* 3.5 15.4 + - - +
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Residues in contact with LEU 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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308C GLN 4.4 0.2 - - - +
311C PHE* 3.7 31.1 - - + +
312C HIS* 3.8 26.0 - - + -
315C MET* 3.9 12.8 - - + -
28D VAL* 3.9 17.5 - - + -
29D LEU* 4.3 7.9 - - + -
32D THR* 4.2 13.9 - - + +
76D ARG 3.2 10.0 + - - +
77D ILE 3.5 7.9 - - - +
78D LEU 3.2 0.2 - - - -
79D ARG* 1.3 78.7 - - - +
81D LEU* 1.3 82.1 + - + +
83D SER* 2.5 31.2 + - - +
84D TYR* 3.5 14.9 + - + -
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Residues in contact with LEU 81 (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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29D LEU* 4.1 17.3 - - + -
32D THR* 4.2 4.3 - - + -
33D LEU* 4.1 27.4 - - + +
36D ALA* 3.5 31.9 - - + -
42D LEU* 4.8 7.4 - - + -
77D ILE* 3.1 22.5 + - + +
78D LEU* 3.3 16.4 + - + +
80D LEU* 1.3 93.2 - - + +
82D ALA* 1.3 58.5 + - - +
84D TYR* 3.2 6.5 + - - -
86D VAL* 2.9 45.6 + - + +
87D VAL* 4.2 6.7 - - + -
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Residues in contact with ALA 82 (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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303C ALA* 5.0 1.0 - - - +
78D LEU 2.8 18.5 + - - +
79D ARG* 3.6 5.8 - - - +
80D LEU 3.1 0.2 - - - -
81D LEU* 1.3 73.0 - - - +
83D SER* 1.3 58.8 + - - +
84D TYR 2.9 6.1 - - - -
85D ASN* 2.9 25.6 + - - -
87D VAL* 3.5 25.8 - - + +
89D CYS* 3.7 29.6 - - + +
103D TYR* 4.4 0.2 - - + -
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Residues in contact with SER 83 (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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303C ALA* 3.4 21.8 - - - +
307C SER* 5.1 2.5 - - - -
308C GLN* 2.7 42.1 + - - +
311C PHE* 3.5 33.9 - - - -
79D ARG 3.2 2.7 + - - -
80D LEU* 2.5 24.7 + - - +
82D ALA* 1.3 76.9 - - - +
84D TYR* 1.3 64.1 + - - +
85D ASN* 3.5 0.4 - - - -
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Residues in contact with TYR 84 (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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19C PHE* 3.5 17.8 - - + -
23C LEU* 5.7 0.4 - - + -
308C GLN* 3.4 27.9 - - + +
312C HIS* 2.7 35.3 + + - -
22D GLN* 3.1 18.6 + - - +
29D LEU* 3.8 45.0 - - + +
80D LEU* 3.7 15.3 - - + -
81D LEU 3.2 8.1 + - - +
82D ALA 2.9 0.8 - - - -
83D SER* 1.3 97.1 + - - +
85D ASN* 1.3 71.2 + - - +
86D VAL* 3.1 11.2 + - + -
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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