Contacts of the helix formed by residues 66 - 84 (chain D) in PDB entry 3DCG
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 66 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C SER* 3.7 16.2 - - - +
23D SER* 3.9 1.1 - - - -
24D SER* 3.5 13.2 - - - +
25D ASP* 3.7 5.4 - - + +
64D GLU 3.5 9.4 - - - +
65D ILE* 1.3 90.2 - - + +
67D SER* 1.3 55.3 + - - +
68D HIS* 3.7 21.8 - - + +
69D VAL* 3.1 16.3 + - + -
70D LEU* 2.8 31.0 + - - +
102D GLU* 4.4 9.4 - - + +
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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
----------------------------------------------------------
93C PHE* 3.7 18.6 - - - -
94C SER* 3.6 15.0 + - - -
23D SER* 3.6 8.4 - - - -
25D ASP* 2.5 40.9 + - - -
27D HIS* 2.6 21.8 + - - +
29D PHE* 3.7 6.2 - - - -
66D PRO* 1.3 71.1 - - - +
68D HIS* 1.3 57.3 + - - +
71D SER* 2.9 35.3 + - - -
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Residues in contact with HIS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C PHE* 4.1 9.2 - - + -
94C SER* 2.6 45.1 + - - +
95C SER 4.0 12.3 - - - -
96C PRO* 3.9 12.1 - - + -
97C PRO* 3.6 7.1 - - + +
66D PRO* 3.7 20.3 - - + +
67D SER* 1.3 79.0 - - - +
69D VAL* 1.3 63.7 + - + +
71D SER* 3.3 14.8 + - - -
72D LYS* 3.9 12.6 + - - +
99D ILE* 3.6 30.8 - - + +
102D GLU* 2.8 30.8 + - - -
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 3.8 7.6 - - + -
66D PRO* 3.1 19.0 + - + +
68D HIS* 1.3 100.5 - - + +
70D LEU* 1.3 60.4 + - - +
71D SER 3.2 1.1 - - - -
72D LYS* 2.9 23.4 + - - +
73D VAL* 3.1 14.6 + - + +
99D ILE* 5.0 6.1 - - + +
102D GLU* 3.6 28.9 - - + +
103D LEU* 3.9 15.0 - - + +
106D ALA* 3.5 31.6 - - + -
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 4.2 26.5 - - + -
22D ILE 3.9 7.0 - - - +
23D SER* 3.6 27.1 - - - +
29D PHE* 3.5 30.5 - - + -
62D PHE* 4.2 17.0 - - + -
65D ILE* 3.9 18.3 - - + +
66D PRO 2.8 20.3 + - - +
69D VAL* 1.3 72.4 - - - +
71D SER* 1.3 60.6 + - - +
73D VAL* 3.4 13.4 + - + +
74D CYS* 3.2 32.3 + - - -
110D LEU* 4.9 9.2 - - + -
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.7 9.8 - - - -
93C PHE* 3.6 31.9 - - - -
29D PHE* 3.7 17.3 - - - -
67D SER 2.9 20.3 + - - -
68D HIS* 3.3 10.4 + - - -
70D LEU* 1.3 78.9 - - - +
72D LYS* 1.3 62.8 + - - +
74D CYS* 3.3 4.9 + - - +
75D MET* 3.2 34.4 + - - +
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 4.8 8.7 + - - -
70C GLN 3.1 26.5 + - - -
68D HIS 4.1 7.4 - - - +
69D VAL 2.9 10.0 + - - +
71D SER* 1.3 77.7 + - - +
73D VAL* 1.3 65.6 + - - +
75D MET* 3.3 18.8 + - + +
76D TYR* 3.0 18.2 + - - +
93D PHE* 3.6 31.2 - - + -
94D PRO* 2.9 34.9 + - - +
95D ILE* 4.8 2.7 - - + +
96D ALA 5.6 0.9 - - - +
99D ILE* 3.6 25.8 - - + -
103D LEU* 4.2 16.6 - - + -
145E LEU* 5.1 0.4 - - - +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 5.4 0.2 - - + -
69D VAL 3.1 17.6 + - - +
70D LEU* 3.6 13.2 - - + +
71D SER 3.3 0.2 - - - -
72D LYS* 1.3 76.0 - - - +
74D CYS* 1.3 57.0 + - - +
76D TYR* 2.9 19.2 + - - +
77D PHE* 3.0 42.5 + - + -
103D LEU* 3.8 18.2 - - + -
106D ALA* 4.4 11.9 - - + -
110D LEU* 3.6 28.5 - - + -
112D CYS* 4.3 1.6 - - - -
145E LEU* 4.0 19.5 - - + -
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Residues in contact with CYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PHE* 3.6 26.2 - - + -
21D LEU* 4.1 18.4 - - - -
29D PHE* 4.0 22.2 - - - -
31D VAL* 3.8 25.7 - - + +
70D LEU* 3.2 18.0 + - - -
71D SER 3.3 3.3 + - - +
73D VAL* 1.3 75.2 - - - +
75D MET* 1.3 61.2 + - - +
77D PHE* 3.3 22.2 + - - +
78D THR* 3.4 16.8 + - - -
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Residues in contact with MET 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 3.9 22.2 - - + +
6C MET* 4.0 21.1 - - + -
15C PHE* 3.7 13.9 - - + -
69C PRO 3.4 18.4 - - - +
70C GLN 3.9 3.4 - - - +
72C PRO* 3.7 28.3 - - + -
93C PHE* 5.3 2.0 - - + -
71D SER* 3.2 27.4 + - - +
72D LYS* 3.6 34.3 - - + +
73D VAL 3.3 0.2 - - - -
74D CYS* 1.3 76.1 - - - +
76D TYR* 1.3 58.4 + - - +
78D THR* 3.5 3.2 + - - +
79D TYR* 3.0 30.0 + - - +
93D PHE* 3.9 9.9 - - + -
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Residues in contact with TYR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D THR* 4.0 17.9 - - + -
72D LYS 3.0 12.3 + - - +
73D VAL 2.9 11.5 + - - +
75D MET* 1.3 74.3 - - - +
77D PHE* 1.3 66.7 + + - +
79D TYR* 3.2 10.2 + + - +
80D LYS* 2.7 58.8 + - + +
93D PHE* 3.7 15.6 - + + -
112D CYS* 3.4 19.3 + - + -
142E VAL* 3.9 11.4 - - + -
143E GLY 2.7 29.5 + - - -
144E SER* 3.4 9.7 - - - -
145E LEU* 3.5 36.6 - - + -
148E LEU* 3.8 15.0 - - + -
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Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 4.2 22.2 - - + -
31D VAL* 4.7 7.0 - - + -
35D HIS* 3.4 22.4 - - + +
36D ALA* 3.8 22.0 - - + -
38D THR* 3.7 19.9 + - + -
39D SER* 3.9 33.0 - - - -
42D ILE* 4.2 7.0 - - + -
73D VAL* 3.0 38.8 + - + -
74D CYS* 3.3 21.7 + - + +
76D TYR* 1.3 77.6 - + - +
78D THR* 1.3 57.9 + - - +
80D LYS* 3.7 1.7 - - - +
81D VAL* 3.0 35.4 + - - +
110D LEU* 4.9 1.6 - - + -
112D CYS* 4.1 11.2 - - - -
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Residues in contact with THR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PHE* 3.6 37.7 - - + -
15C PHE* 5.2 11.0 - - - +
17C ASP* 5.3 2.5 - - - +
69C PRO* 3.8 12.6 - - + -
31D VAL* 5.9 1.2 - - - +
35D HIS* 3.8 26.1 + - + +
74D CYS 3.4 10.8 + - - -
75D MET* 3.8 6.9 - - - -
76D TYR 3.3 0.4 - - - -
77D PHE* 1.3 74.4 - - - +
79D TYR* 1.3 61.2 + - - +
81D VAL* 3.4 1.7 + - - +
82D ARG* 3.0 30.2 + - + +
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Residues in contact with TYR 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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69C PRO* 3.8 12.5 - - + +
70C GLN* 3.0 31.6 - - + -
75D MET 3.0 18.7 + - - +
76D TYR* 3.4 12.6 - + - +
78D THR* 1.3 76.2 - - - +
80D LYS* 1.3 63.6 + - - +
82D ARG 3.3 0.7 + - - -
83D TYR* 3.0 52.9 + + - +
90D ILE* 3.2 15.5 - - + +
91D PRO* 2.7 29.1 + - + -
92D GLU* 4.5 0.2 - - - -
93D PHE* 3.7 37.1 + + + +
142E VAL* 3.5 26.0 - - + +
148E LEU* 4.5 8.3 - - + +
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Residues in contact with LYS 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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38D THR* 3.6 30.7 - - + +
76D TYR* 2.7 48.6 + - + +
77D PHE 3.7 4.3 - - - +
79D TYR* 1.3 73.7 - - - +
81D VAL* 1.3 57.5 + - + +
84D THR* 3.0 51.4 + - - +
112D CYS* 5.4 1.8 - - - -
142E VAL* 3.6 34.4 + - + +
144E SER* 5.8 1.1 - - - +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLU 4.9 3.6 - - - +
35D HIS* 4.0 39.9 - - + +
38D THR* 4.0 15.7 - - - +
77D PHE 3.0 21.4 + - - +
78D THR 4.0 3.1 - - - +
80D LYS* 1.3 78.5 - - + +
82D ARG* 1.3 63.5 + - - +
84D THR* 4.2 13.3 + - - +
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Residues in contact with ARG 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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2C ASP* 2.7 42.5 + - - +
4C PHE* 3.6 32.1 - - + -
64C SER* 5.9 0.6 + - - -
69C PRO* 4.0 6.5 - - + +
78D THR* 3.0 19.3 + - + +
79D TYR 3.5 4.7 - - - +
80D LYS 3.3 0.2 - - - -
81D VAL* 1.3 80.9 - - + +
83D TYR* 1.3 93.9 + - + +
84D THR 3.7 4.0 + - - +
86D SER* 5.1 2.9 + - - -
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Residues in contact with TYR 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ARG* 5.4 2.1 - - - +
69C PRO* 4.1 11.5 - - + +
70C GLN* 3.7 25.6 + - - -
79D TYR* 3.0 40.3 + + - +
82D ARG* 1.3 105.5 + - + +
84D THR* 1.3 61.9 + - - +
86D SER* 3.2 25.9 - - - -
89D GLU 5.7 0.4 - - - -
90D ILE* 3.5 29.1 - - + +
91D PRO* 3.5 32.9 - - + +
140E ASN 3.1 16.6 - - - +
142E VAL* 3.6 7.9 - - + -
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LYS* 3.0 40.5 + - - +
81D VAL* 4.5 10.5 - - - +
82D ARG 3.5 5.4 - - - +
83D TYR* 1.3 77.0 - - - +
85D ASN* 1.3 81.7 + - - +
86D SER 3.5 0.2 + - - -
140E ASN 4.0 0.7 - - - -
141E LYS* 4.8 5.9 + - - +
142E VAL* 3.8 14.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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