Contacts of the helix formed by residues 98 - 115 (chain B) in PDB entry 3G33
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 GLN 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 4.4 6.6 - - - -
95B ARG* 3.2 42.8 + - + +
96B LYS 3.2 1.2 - - - -
97B ALA* 1.3 80.0 - - + +
99B LEU* 1.3 58.6 + - - +
100B GLN 3.4 1.8 - - - -
101B LEU* 3.4 14.1 + - + +
102B LEU* 3.0 29.7 + - - +
140B TRP* 3.6 36.6 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 6.0 11.0 - - + -
56B MET* 3.9 50.3 - - + +
57B ARG* 5.3 2.9 - - - -
60B LEU* 3.7 26.4 - - + +
85B LEU* 4.9 3.8 - - + -
89B LEU* 5.0 12.6 - - + -
94B THR* 5.6 2.5 - - - +
95B ARG 3.5 5.6 + - - +
96B LYS* 3.2 17.3 + - - +
97B ALA 3.2 0.2 - - - -
98B GLN* 1.3 77.7 - - - +
100B GLN* 1.3 58.4 + - - +
102B LEU* 3.2 20.3 + - + +
103B GLY* 2.9 26.2 + - - -
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.2 12.1 - - + +
63B TRP* 4.0 32.0 + - + -
96B LYS 4.8 0.2 + - - -
97B ALA 4.5 5.2 + - - +
98B GLN 3.4 0.2 - - - -
99B LEU* 1.3 78.4 - - - +
101B LEU* 1.3 61.3 + - - +
103B GLY* 3.3 1.7 + - - -
104B ALA* 3.1 22.9 + - - +
127B TYR 4.5 1.2 - - - +
128B THR* 3.7 29.7 + - + +
131B ALA* 4.2 21.8 - - - +
132B VAL* 4.6 4.6 - - + +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA 4.9 1.5 + - - +
98B GLN* 3.4 18.2 + - + +
99B LEU 3.2 0.2 - - - -
100B GLN* 1.3 79.8 - - - +
102B LEU* 1.3 63.7 + - - +
104B ALA* 3.3 4.8 + - - +
105B VAL* 3.3 18.2 + - - +
132B VAL* 3.5 40.4 - - + +
136B GLN* 4.0 33.2 - - + +
137B LEU* 3.8 12.6 - - + -
140B TRP* 3.2 50.3 - - + +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.6 26.5 - - + -
88B TYR* 3.6 42.6 - - + -
89B LEU* 3.8 15.9 - - + -
94B THR* 4.1 6.7 - - - +
98B GLN 3.0 13.9 + - - +
99B LEU* 3.2 14.1 + - + +
101B LEU* 1.3 76.4 - - - +
103B GLY* 1.3 63.1 + - - +
105B VAL* 3.3 4.2 + - - +
106B CYS* 3.2 29.9 + - - -
140B TRP* 4.3 13.7 - - + -
144B VAL* 3.8 24.7 - - + -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 4.3 6.3 - - - +
63B TRP* 4.5 4.7 - - - -
64B MET* 3.2 33.2 - - - +
85B LEU* 4.9 0.4 - - - -
99B LEU 2.9 13.0 + - - -
100B GLN 3.3 3.6 + - - -
101B LEU 3.2 0.6 - - - -
102B LEU* 1.3 78.6 - - - +
104B ALA* 1.3 61.9 + - - +
106B CYS* 3.4 4.5 + - - +
107B MET* 3.0 22.1 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TRP* 4.3 5.6 - - + -
100B GLN 3.1 12.7 + - - +
101B LEU* 3.3 9.6 + - - +
103B GLY* 1.3 75.0 - - - +
105B VAL* 1.3 52.9 + - - +
107B MET* 3.1 14.8 - - - +
108B LEU* 2.7 35.4 + - - +
124B LEU* 3.6 17.9 - - + +
128B THR* 4.4 18.4 - - + -
132B VAL* 5.5 0.2 - - + -
137B LEU* 3.9 17.3 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU 3.3 14.7 + - - +
102B LEU* 3.6 7.2 - - - +
103B GLY 3.3 0.2 - - - -
104B ALA* 1.3 75.8 - - - +
106B CYS* 1.3 59.1 + - - +
108B LEU* 3.0 9.7 + - + +
109B LEU* 2.8 40.2 + - + +
137B LEU* 3.8 19.1 - - + +
140B TRP* 3.6 28.7 - - + -
141B GLU* 3.6 29.2 - - + +
144B VAL* 3.6 22.4 - - + -
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Residues in contact with CYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 5.1 1.6 - - + -
81B ALA* 3.4 22.7 - - + +
84B TYR* 3.7 18.8 - - + -
85B LEU* 3.6 34.5 - - + -
88B TYR* 5.6 0.2 - - - -
102B LEU* 3.2 30.7 + - - -
103B GLY* 3.7 8.3 - - - +
105B VAL* 1.3 78.3 - - - +
107B MET* 1.3 63.9 + - - +
109B LEU* 4.6 2.7 - - - -
110B ALA* 2.8 27.2 + - - +
144B VAL* 4.8 7.6 - - - -
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Residues in contact with MET 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TRP* 3.7 23.6 - - + -
64B MET* 3.6 59.2 - - + +
67B VAL* 4.0 16.4 - - + -
68B CYS* 3.8 15.9 - - - -
77B VAL* 4.1 2.8 - - + +
81B ALA* 3.8 11.8 - - + +
103B GLY 3.0 9.4 + - - +
104B ALA* 3.1 11.7 - - - +
106B CYS* 1.3 76.8 - - - +
108B LEU* 1.3 64.4 + - - +
110B ALA* 3.3 1.7 + - - +
111B SER* 2.9 25.2 + - - -
119B LEU* 4.1 12.3 - - + -
124B LEU* 4.0 17.5 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA 2.7 16.6 + - - +
105B VAL* 3.2 10.1 - - - +
107B MET* 1.3 73.8 - - - +
109B LEU* 1.3 58.3 + - - +
111B SER* 3.1 5.6 + - - -
112B LYS* 2.8 51.7 + - + +
119B LEU* 3.1 30.1 - - - +
121B ILE* 4.2 27.1 - - + -
124B LEU* 3.7 15.6 - - + +
137B LEU* 4.7 13.5 - - + +
138B ARG* 6.4 0.2 - - - -
141B GLU* 3.7 35.9 - - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 4.0 12.8 - - + -
105B VAL* 2.8 28.8 + - + +
106B CYS* 3.8 5.2 - - - +
108B LEU* 1.3 72.2 - - - +
110B ALA* 1.3 65.4 + - - +
112B LYS* 2.9 19.2 + - + +
113B LEU* 3.0 15.7 + - - +
141B GLU* 3.7 33.4 - - + +
144B VAL* 3.9 31.2 - - + -
145B LEU* 4.0 22.4 - - + -
152B LEU* 4.0 24.7 - - + +
59C VAL* 4.5 9.4 - - + +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.5 32.4 - - + +
80B LEU* 4.0 10.2 - - + +
81B ALA* 3.6 13.0 - - - +
84B TYR* 3.4 14.6 - - + -
106B CYS 2.8 21.7 + - - +
107B MET 3.5 3.6 - - - +
109B LEU* 1.3 74.6 - - - +
111B SER* 1.3 63.4 + - - +
113B LEU* 3.3 2.9 + - - +
114B ARG* 3.2 24.8 + - - +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.8 14.7 - - - +
107B MET 2.9 13.0 + - - -
108B LEU 3.4 7.9 - - - -
110B ALA* 1.3 74.3 - - - +
112B LYS* 1.3 67.0 + - - +
113B LEU 3.0 0.2 + - - -
115B GLU* 2.8 49.9 + - - +
118B PRO* 3.1 7.2 - - - +
119B LEU* 3.0 38.6 + - - +
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 2.8 40.2 + - + +
109B LEU* 3.4 13.9 - - + +
111B SER* 1.3 72.6 - - - +
113B LEU* 1.3 57.0 + - - +
118B PRO* 3.5 16.8 - - + -
119B LEU 5.0 2.0 - - - -
121B ILE* 5.8 0.7 - - - -
141B GLU* 2.6 28.0 + - - +
53C GLY* 3.6 6.0 - - - -
54C LEU* 2.5 52.2 - - + +
56C ILE* 2.6 50.2 - - + +
59C VAL* 5.3 9.4 - - + -
60C ARG* 3.0 7.0 + - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 4.4 7.6 - - + -
84B TYR* 3.5 9.4 - - - +
109B LEU 3.0 14.8 + - - +
110B ALA 3.7 4.0 - - - +
111B SER 3.0 0.2 - - - -
112B LYS* 1.3 78.9 - - - +
114B ARG* 1.3 66.1 + - + +
152B LEU* 3.0 38.4 - - + +
153B ALA* 3.7 10.8 - - + +
59C VAL* 4.0 17.5 - - + +
60C ARG* 3.3 50.1 + - + +
63C ALA* 4.1 10.1 - - + -
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 3.9 11.8 - - + +
76B GLU* 3.1 43.3 + - + +
77B VAL* 4.8 7.0 - - + -
80B LEU* 3.3 28.6 - - + +
110B ALA 3.2 12.4 + - - +
111B SER 3.1 2.2 + - - -
113B LEU* 1.3 86.9 - - - +
115B GLU* 1.3 63.8 + - - +
153B ALA* 4.6 4.0 - - - +
154B ALA 3.1 30.5 + - - +
156B ILE* 4.7 2.9 - - - +
159B ASP* 2.8 33.3 + - - -
60C ARG* 4.4 1.3 - - - -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG 4.7 0.9 - - - +
73B CYS* 3.3 29.7 - - - +
74B GLU* 3.2 34.6 + - + +
77B VAL* 3.4 18.1 - - + +
111B SER* 2.8 32.4 + - - +
114B ARG* 1.3 83.7 - - - +
116B THR* 1.3 63.8 + - - +
117B THR 3.5 8.6 + - - +
118B PRO* 3.5 15.9 - - + +
119B LEU* 4.6 1.7 - - - +
60C ARG* 2.7 25.7 + - - +
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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