Contacts of the helix formed by residues 95 - 111 (chain D) in PDB entry 2G33
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 LEU 95 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D SER* 3.3 40.6 - - - +
24D PHE* 5.5 2.6 - - + -
89D VAL 4.2 1.0 + - - -
90D ASN 5.0 0.4 - - - -
91D THR 3.7 26.8 + - - +
92D ASN* 4.3 9.6 - - - +
93D VAL 2.5 0.8 - - - -
94D GLY* 1.3 75.4 - - - +
96D LYS* 1.3 64.0 + - + +
97D PHE 3.0 1.3 - - - -
98D ARG* 2.9 27.2 + - - +
99D GLN* 2.7 52.1 + - + +
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Residues in contact with LYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 6.3 0.4 - - - +
64C ASP* 3.0 39.4 + - - +
6D TYR* 5.0 0.3 + - - -
92D ASN 4.4 6.5 + - - +
93D VAL* 2.7 33.9 + - + +
95D LEU* 1.3 79.9 - - + +
97D PHE* 1.3 61.6 + - + +
99D GLN* 3.4 21.5 - - - +
100D LEU* 3.2 27.4 + - - +
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Residues in contact with PHE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 4.1 25.4 - - + -
64C ASP* 4.2 19.5 - - + -
27D VAL* 5.9 2.5 - - + -
58D ALA* 3.7 21.5 - - + -
61D ALA* 4.8 1.8 - - + -
62D TRP* 3.5 59.7 - + + -
65D LEU* 4.5 9.0 - - + -
93D VAL* 2.9 20.8 + - + +
94D GLY 3.9 3.1 - - - +
96D LYS* 1.3 90.5 - - + +
98D ARG* 1.3 55.6 + - - +
99D GLN 3.3 0.2 - - - -
100D LEU* 4.8 12.6 - - + +
101D LEU* 2.8 46.5 + - + +
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Residues in contact with ARG 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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21D SER* 3.6 22.8 + - - -
22D ASP* 5.0 3.6 - - - +
23D PHE 4.8 2.4 - - - +
24D PHE* 2.7 47.5 + - + +
25D PRO 3.2 20.5 - - - +
26D SER* 4.3 4.2 - - - +
27D VAL* 3.7 23.8 - - + +
30D LEU* 3.7 5.6 - - + +
90D ASN 4.8 11.5 + - - -
91D THR 5.5 0.8 + - - -
94D GLY 3.1 22.0 + - - +
95D LEU* 2.9 28.0 + - - +
97D PHE* 1.3 75.3 - - - +
99D GLN* 1.3 72.2 + - - +
101D LEU* 3.4 4.2 - - - +
102D TRP* 3.1 20.3 + - - +
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Residues in contact with GLN 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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6D TYR* 4.4 6.6 + - - +
13D VAL* 4.8 15.5 + - - +
16D LEU* 3.5 41.6 + - + +
17D SER* 4.9 1.0 - - - +
19D LEU 5.7 0.2 + - - -
24D PHE* 3.7 36.9 - - + -
95D LEU* 2.7 28.3 + - + +
96D LYS* 3.4 26.0 - - - +
98D ARG* 1.3 83.9 - - - +
100D LEU* 1.3 71.8 + - - +
102D TRP* 2.8 8.2 + - - +
103D PHE* 3.3 8.7 + - - -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN* 3.5 28.9 - - - +
5D PRO* 5.0 12.6 - - + +
6D TYR* 3.2 24.6 + - + +
54D ALA* 6.5 0.2 - - + -
55D LEU* 5.8 3.4 - - + +
58D ALA* 4.2 22.0 - - + -
96D LYS 3.2 13.9 + - - +
97D PHE* 4.8 12.8 - - + +
99D GLN* 1.3 80.7 - - - +
101D LEU* 1.3 91.1 + - + +
103D PHE* 2.8 23.5 + - - +
104D HIS* 3.7 22.3 + - + +
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Residues in contact with LEU 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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27D VAL* 4.4 11.7 - - + -
30D LEU* 3.3 35.9 - - + -
31D LEU* 4.3 26.2 - - + +
34D ALA* 6.1 1.6 - - + -
55D LEU* 5.6 2.4 - - - +
58D ALA* 5.8 4.5 - - + -
59D ILE* 5.7 14.1 - - + +
62D TRP* 5.8 4.7 - - + -
97D PHE* 2.8 34.1 + - + +
98D ARG* 3.4 4.9 - - - +
99D GLN 2.9 2.0 + - - -
100D LEU* 1.3 89.2 - - + +
102D TRP* 1.3 65.7 + - - +
104D HIS* 3.8 7.3 + - - +
105D ILE* 3.2 26.0 + - + +
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Residues in contact with TRP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 5.8 2.7 - - + -
19D LEU* 4.4 15.0 - - + -
23D PHE* 4.6 23.5 - + - -
24D PHE* 3.8 31.6 - + + -
25D PRO* 5.4 9.9 - - + -
30D LEU* 3.6 16.5 - - + +
98D ARG 3.1 7.1 + - - +
99D GLN 2.8 12.4 + - - +
101D LEU* 1.3 75.9 - - - +
103D PHE* 1.3 100.9 + + + +
104D HIS 2.8 1.9 + - - -
105D ILE* 3.1 20.2 + - + +
106D SER* 3.1 32.9 + - - -
115D VAL* 5.6 5.2 - - + -
118D TYR* 5.3 15.3 - + - -
119D LEU* 5.2 16.4 - - + -
140D LEU* 5.0 18.5 - - + +
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Residues in contact with PHE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D TYR* 4.0 34.5 - + + -
9D PHE* 4.3 30.1 - + + -
11D ALA* 4.6 9.2 - - + -
16D LEU* 5.5 7.4 - - + -
51D HIS* 4.9 5.8 - + - -
99D GLN 3.3 2.4 + - - +
100D LEU* 2.8 22.0 + - - +
102D TRP* 1.3 104.8 - + + +
104D HIS* 1.3 100.9 + + - +
106D SER* 2.9 18.0 + - - -
107D ALA* 3.6 7.8 + - + +
112D ARG* 6.0 2.2 - - + -
115D VAL* 4.6 14.0 - - + +
116D LEU* 4.6 19.3 - - + -
119D LEU* 5.4 7.2 - - + -
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Residues in contact with HIS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN* 5.4 3.4 + - - -
5D PRO 5.4 3.8 + - - -
6D TYR* 5.8 0.6 - - - -
9D PHE* 3.8 30.7 - + - -
51D HIS* 3.1 29.7 + - - +
54D ALA* 3.8 19.6 - - + +
55D LEU* 3.8 26.5 - - + -
100D LEU* 3.9 33.7 - - + +
101D LEU 4.0 5.8 - - - +
102D TRP 2.8 2.0 + - - -
103D PHE* 1.3 97.1 - + - +
105D ILE* 1.3 69.6 + - - +
106D SER 2.5 2.9 + - - -
107D ALA* 2.7 18.9 + - - +
108D LEU* 2.9 13.8 + - + -
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Residues in contact with ILE 105 (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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30D LEU* 4.7 16.8 - - + +
33D THR* 4.3 22.2 - - + -
34D ALA* 4.8 11.4 - - + -
37D LEU* 5.7 1.8 - - + -
38D TYR* 4.1 15.4 + - + -
55D LEU* 5.0 11.4 - - + +
101D LEU* 3.2 41.5 - - + +
102D TRP* 3.1 14.5 + - + +
104D HIS* 1.3 72.9 - - + +
106D SER* 1.3 59.8 + - - +
108D LEU* 3.0 18.0 - - - +
109D THR* 2.7 29.8 + - - +
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Residues in contact with SER 106 (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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102D TRP* 3.1 41.1 + - - -
103D PHE 2.9 13.8 + - - -
104D HIS 2.5 3.2 + - - -
105D ILE* 1.3 68.3 - - - +
107D ALA* 1.3 51.6 + - - -
108D LEU 2.6 4.0 + - - -
109D THR 2.5 27.9 + - - -
110D PHE* 2.7 34.2 + - - -
115D VAL* 4.6 10.5 - - - -
140D LEU* 5.1 9.0 - - - -
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Residues in contact with ALA 107 (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 HIS* 4.3 16.5 + - + +
103D PHE* 3.6 8.2 + - + +
104D HIS* 2.7 10.2 + - - +
106D SER* 1.3 76.0 - - - +
108D LEU* 1.3 56.8 + - - +
109D THR 3.0 2.1 + - - -
110D PHE 3.6 0.9 - - - -
111D GLY* 2.9 24.5 + - - +
112D ARG* 3.4 33.1 + - + +
115D VAL* 3.4 18.9 - - + +
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Residues in contact with LEU 108 (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 TYR* 3.2 36.1 + - + +
42D LEU* 6.4 0.7 - - + -
51D HIS* 3.0 46.7 - - + +
52D HIS* 3.9 33.7 - - + +
55D LEU* 5.0 13.7 - - + -
104D HIS* 2.9 14.2 + - + +
105D ILE* 3.0 16.2 - - - +
106D SER 2.6 3.6 + - - -
107D ALA* 1.3 74.1 - - - +
109D THR* 1.3 62.0 + - - +
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Residues in contact with THR 109 (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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37D LEU* 5.1 12.1 - - + +
38D TYR* 3.0 14.4 + - - +
105D ILE* 2.7 19.9 + - - +
106D SER 2.5 7.7 + - - -
108D LEU* 1.3 74.9 - - - +
110D PHE* 1.3 85.3 + - + +
111D GLY 3.9 1.1 - - - -
142D THR* 4.1 11.6 - - - +
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Residues in contact with PHE 110 (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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106D SER* 2.7 39.7 + - - +
107D ALA* 3.9 0.9 - - - -
109D THR* 1.3 104.6 - - + +
111D GLY* 1.3 66.5 + - - +
114D THR* 2.7 31.8 - - + +
115D VAL* 4.4 7.4 - - + -
140D LEU* 3.3 57.4 - - + -
141D SER 4.7 2.9 - - - -
142D THR* 4.0 25.6 - - + -
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Residues in contact with GLY 111 (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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107D ALA* 2.9 14.3 + - - -
109D THR 3.9 1.0 - - - -
110D PHE* 1.3 84.4 - - - +
112D ARG* 1.3 70.1 + - - -
113D GLU* 3.1 3.6 - - - -
114D THR* 2.8 14.5 + - - -
115D VAL* 2.8 6.2 + - - +
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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
------------------------------------------------------------
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