Contacts of the helix formed by residues 81 - 101 (chain D) in PDB entry 3T79
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 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D ASP* 5.5 1.3 - - - -
80D ILE* 1.3 78.8 - - - +
82D ASN* 1.3 71.5 + - - +
83D ASN* 1.9 42.5 + - - +
84D ASP* 3.1 17.2 + - + +
85D VAL* 2.9 25.5 + - - +
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Residues in contact with ASN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 4.3 12.5 + - - +
80D ILE 3.8 1.7 + - - -
81D GLU* 1.3 79.0 + - - +
83D ASN* 1.3 65.7 + - - +
84D ASP 3.1 0.7 - - - -
85D VAL* 2.6 35.7 - - - +
86D LEU* 2.9 15.3 + - - +
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLU* 1.9 44.0 + - - +
82D ASN* 1.3 72.8 - - - +
84D ASP* 1.3 65.7 + - - -
86D LEU* 2.9 26.1 + - + +
87D VAL* 2.6 31.8 + - + +
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Residues in contact with ASP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ILE* 3.2 21.7 - - - +
81D GLU* 3.1 25.1 + - + +
83D ASN* 1.3 83.2 + - - +
85D VAL* 1.3 65.5 + - - +
87D VAL* 2.7 41.7 - - - +
88D LEU* 3.0 4.2 + - - +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 3.6 31.8 - - + +
75D SER* 3.5 25.1 - - - +
76D ARG* 4.0 26.0 - - + +
80D ILE* 4.0 9.0 - - + +
81D GLU 2.9 18.9 + - - +
82D ASN* 2.6 41.5 - - - +
84D ASP* 1.3 72.1 - - - +
86D LEU* 1.3 57.1 + - - +
88D LEU* 3.0 11.8 + - + +
89D GLN* 2.9 24.4 + - - +
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 5.7 3.6 - - - +
82D ASN* 2.9 15.0 + - - +
83D ASN* 3.0 40.2 - - + +
85D VAL* 1.3 76.7 - - + +
87D VAL* 1.3 62.5 + - + +
89D GLN* 3.2 14.1 - - - +
90D GLN* 2.1 56.1 + - + +
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN* 3.7 20.2 - - - +
83D ASN* 2.6 37.7 + - + +
84D ASP* 2.7 24.9 - - - +
86D LEU* 1.3 76.1 - - + +
88D LEU* 1.3 71.1 + - + +
90D GLN* 2.5 36.0 + - - +
91D ARG* 2.9 10.9 + - - +
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Residues in contact with LEU 88 (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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45D LEU* 5.4 5.8 - - + +
46D SER* 5.1 2.9 - - - -
47D GLN* 4.1 30.7 - - + +
50D ILE* 3.9 24.9 - - + -
71D MET* 5.2 1.3 - - + +
72D ILE* 4.4 15.0 - - + +
75D SER* 5.1 13.5 - - - +
84D ASP* 3.0 7.9 + - - +
85D VAL* 3.0 13.4 + - + +
87D VAL* 1.3 85.9 - - + +
89D GLN* 1.3 57.8 + - - +
91D ARG* 3.3 1.7 + - - +
92D LEU* 2.9 57.6 + - + +
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Residues in contact with GLN 89 (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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72D ILE* 3.7 37.5 - - + +
76D ARG* 4.8 8.7 + - - -
85D VAL 2.9 11.0 + - - +
86D LEU* 3.2 17.7 - - - +
88D LEU* 1.3 74.3 - - - +
90D GLN* 1.3 73.3 + - - +
92D LEU* 3.3 2.3 + - - +
93D TYR* 2.9 67.5 + - + +
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Residues in contact with GLN 90 (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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86D LEU* 2.1 55.1 + - + +
87D VAL* 2.5 22.5 + - - +
89D GLN* 1.3 80.3 - - - +
91D ARG* 1.3 60.7 + - - +
93D TYR* 3.9 9.0 - - - +
94D GLY* 3.0 20.4 + - - -
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Residues in contact with ARG 91 (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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47D GLN* 3.9 33.9 + - + +
51D VAL* 3.4 44.0 - - + +
87D VAL 2.9 5.4 + - - +
88D LEU 3.5 8.1 - - - +
90D GLN* 1.3 74.9 - - - +
92D LEU* 1.3 65.9 + - + +
94D GLY* 3.0 5.3 + - - -
95D LEU* 2.8 28.1 + - - +
279D PRO* 3.4 38.1 - - - +
281D PHE* 4.5 7.9 - - - -
303D PRO* 4.2 12.5 - - - +
306D TYR* 2.2 45.9 + - - -
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Residues in contact with LEU 92 (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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47D GLN* 5.9 1.8 - - - -
50D ILE* 4.2 21.5 - - + -
51D VAL* 4.5 18.6 - - + -
54D ILE* 4.6 4.9 - - + -
68D CYS* 3.7 51.3 - - + +
71D MET* 4.6 6.1 - - + -
72D ILE* 4.3 4.7 - - + -
88D LEU* 2.9 48.6 + - + +
89D GLN* 3.7 3.6 - - - +
91D ARG* 1.3 73.1 - - + +
93D TYR* 1.3 66.4 + - + +
95D LEU* 2.9 11.9 + - + +
96D VAL* 2.9 25.0 + - - +
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Residues in contact with TYR 93 (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 LEU* 4.4 19.2 - - + +
68D CYS* 5.0 4.5 - - + -
69D ASP* 3.8 21.4 + - - -
72D ILE* 4.3 8.4 - - + +
89D GLN* 2.9 62.0 + - + +
90D GLN* 3.9 9.4 - - - +
92D LEU* 1.3 75.2 - - + +
94D GLY* 1.3 63.0 + - - +
96D VAL* 3.1 10.9 + - + +
97D LYS* 3.0 35.1 + - - +
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Residues in contact with GLY 94 (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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90D GLN 3.0 15.2 + - - -
91D ARG* 3.0 4.9 + - - -
93D TYR* 1.3 72.1 - - - +
95D LEU* 1.3 66.0 + - - +
97D LYS* 3.6 11.6 + - - +
98D LEU* 3.0 21.8 + - - +
277D GLN* 4.8 19.7 + - - +
306D TYR* 4.4 2.9 - - - -
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Residues in contact with LEU 95 (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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51D VAL* 4.1 30.7 - - + +
54D ILE* 4.0 33.0 - - + -
55D ALA* 5.0 1.3 - - + +
91D ARG* 2.8 13.5 + - - +
92D LEU* 2.9 14.3 + - + +
94D GLY* 1.3 74.1 - - - +
96D VAL* 1.3 59.9 + - + +
98D LEU* 2.6 29.6 + - + +
99D LEU* 2.9 41.3 + - + +
305D PHE* 4.5 12.6 - - + -
306D TYR* 3.5 19.0 + - - +
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Residues in contact with VAL 96 (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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64D PRO* 4.0 28.5 - - + -
65D LEU* 4.8 22.7 - - + -
68D CYS* 4.0 22.7 - - - -
92D LEU 2.9 23.4 + - - +
93D TYR* 3.1 10.5 + - + +
95D LEU* 1.3 75.6 - - + +
97D LYS* 1.3 64.8 + - + +
99D LEU* 3.0 5.2 + - + +
100D GLU* 2.9 45.9 + - + +
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Residues in contact with LYS 97 (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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93D TYR* 3.0 19.8 + - - +
94D GLY* 3.7 12.5 - - - +
96D VAL* 1.3 75.3 - - + +
98D LEU* 1.3 65.1 + - - +
100D GLU* 3.7 17.5 - - - +
101D PHE* 2.8 34.3 + - + +
273D GLN* 3.1 39.6 + - - +
274D GLU* 4.8 7.2 - - - +
275D TRP 4.0 6.9 + - - +
276D PRO* 4.5 12.1 - - + -
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Residues in contact with LEU 98 (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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94D GLY 3.0 13.5 + - - +
95D LEU* 2.6 20.7 + - + +
97D LYS* 1.3 73.5 - - - +
99D LEU* 1.3 59.4 + - + +
101D PHE* 4.8 0.2 - - - -
276D PRO* 4.1 22.3 - - + +
277D GLN 4.9 0.9 - - - +
305D PHE* 4.9 6.1 - - + +
306D TYR* 3.0 68.2 - - + +
309D LYS* 3.1 49.9 - - + +
310D MET* 4.5 9.6 - - + +
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Residues in contact with LEU 99 (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 ILE* 4.3 7.6 - - + +
55D ALA* 5.1 5.4 - - + -
61D ALA* 3.5 42.4 - - + +
64D PRO* 4.0 15.3 - - + -
95D LEU* 2.9 44.2 + - + -
96D VAL* 3.6 5.6 - - - +
98D LEU* 1.3 76.0 - - + +
100D GLU* 1.3 63.4 + - + +
305D PHE* 4.3 22.0 - - + -
309D LYS* 4.2 9.8 + - - +
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Residues in contact with GLU 100 (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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96D VAL* 2.9 35.0 + - + +
97D LYS* 3.5 20.7 + - - +
99D LEU* 1.3 78.3 - - + +
101D PHE* 1.3 71.9 + - - +
102D ASP* 3.3 5.5 + - - +
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Residues in contact with PHE 101 (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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385A GLU 5.6 1.6 - - - -
388A GLU* 4.4 9.9 - - - -
97D LYS* 2.8 23.4 + - + +
98D LEU 4.3 4.7 - - - +
99D LEU 3.4 1.0 - - - -
100D GLU* 1.3 81.9 - - + +
102D ASP* 1.3 81.3 + - - +
103D TYR* 3.5 26.9 - + - -
106D VAL* 3.9 12.3 - - + -
274D GLU* 3.4 17.3 - - + -
275D TRP* 3.3 42.4 - + - -
276D PRO* 3.5 20.9 - - + -
309D LYS* 2.3 38.5 + - - -
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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