Contacts of the helix formed by residues 98 - 115 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D THR* 4.4 7.1 - - - -
95D ARG* 3.2 42.9 + - + +
96D LYS 3.1 1.2 - - - -
97D ALA* 1.3 80.3 - - + +
99D LEU* 1.3 58.5 + - - +
100D GLN 3.4 1.8 - - - -
101D LEU* 3.4 13.5 + - + +
102D LEU* 3.0 29.7 + - - +
140D TRP* 3.6 38.0 - - + -
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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
----------------------------------------------------------
52D ILE* 6.0 10.8 - - + -
56D MET* 3.9 50.0 - - + +
57D ARG* 5.0 2.9 - - - +
60D LEU* 3.7 26.5 - - + +
85D LEU* 4.9 3.8 - - + -
89D LEU* 5.0 13.0 - - + -
94D THR* 5.6 2.5 - - - +
95D ARG 3.5 5.1 + - - +
96D LYS* 3.2 17.3 + - - +
98D GLN* 1.3 76.1 - - - +
100D GLN* 1.3 61.7 + - - +
102D LEU* 3.2 19.3 + - + +
103D GLY* 2.9 26.0 + - - -
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Residues in contact with GLN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 4.2 11.6 - - + +
63D TRP* 4.0 31.7 + - + -
96D LYS 4.8 0.2 + - - -
97D ALA 4.5 5.9 + - - +
98D GLN 3.4 0.4 - - - -
99D LEU* 1.3 78.4 - - - +
101D LEU* 1.3 63.7 + - - +
103D GLY* 3.3 1.6 + - - -
104D ALA* 3.1 22.2 + - - +
127D TYR 4.5 0.9 - - - +
128D THR* 3.7 29.2 + - + +
131D ALA* 4.2 21.6 - - - +
132D VAL* 4.6 5.3 - - + +
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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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97D ALA 4.9 1.3 + - - +
98D GLN* 3.4 17.8 + - + +
99D LEU 3.2 0.2 - - - -
100D GLN* 1.3 79.3 - - - +
102D LEU* 1.3 62.8 + - - +
104D ALA* 3.3 3.9 + - - +
105D VAL* 3.2 18.7 + - - +
132D VAL* 3.5 40.4 - - + +
136D GLN* 4.0 32.8 - - + +
137D LEU* 3.8 13.7 - - + -
140D TRP* 3.2 51.8 - - + +
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LEU* 3.6 25.8 - - + -
88D TYR* 3.6 42.0 - - + -
89D LEU* 3.8 16.4 - - + -
94D THR* 4.1 7.0 - - - +
98D GLN 3.0 14.3 + - - +
99D LEU* 3.5 13.9 - - + +
101D LEU* 1.3 76.8 - - - +
103D GLY* 1.3 63.7 + - - +
105D VAL* 3.3 3.9 + - - +
106D CYS* 3.2 29.0 + - - -
140D TRP* 4.3 14.1 - - + -
144D VAL* 3.8 25.1 - - + -
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Residues in contact with GLY 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 4.3 5.1 - - - +
63D TRP* 4.5 4.9 - - - -
64D MET* 3.2 33.8 - - - +
85D LEU* 4.9 0.9 - - - -
99D LEU 2.9 13.3 + - - -
100D GLN 3.3 4.0 + - - -
101D LEU 3.2 0.6 - - - -
102D LEU* 1.3 78.7 - - - +
104D ALA* 1.3 62.3 + - - +
106D CYS* 3.4 4.1 + - - +
107D MET* 3.0 23.0 + - - +
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Residues in contact with ALA 104 (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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63D TRP* 4.3 5.9 - - + -
100D GLN 3.1 13.3 + - - +
101D LEU* 3.3 8.9 + - - +
103D GLY* 1.3 74.6 - - - +
105D VAL* 1.3 53.6 + - - +
107D MET* 3.1 14.0 - - - +
108D LEU* 2.7 35.6 + - - +
124D LEU* 3.5 18.0 - - + +
128D THR* 4.4 18.4 - - + -
132D VAL* 5.5 0.2 - - + -
137D LEU* 3.9 17.3 - - + -
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Residues in contact with VAL 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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101D LEU 3.2 15.6 + - - +
102D LEU* 3.6 7.2 - - - +
103D GLY 3.3 0.2 - - - -
104D ALA* 1.3 77.1 - - - +
106D CYS* 1.3 58.2 + - - +
108D LEU* 3.0 9.1 + - - +
109D LEU* 2.8 39.6 + - + +
137D LEU* 3.8 19.3 - - + +
140D TRP* 3.6 28.3 - - + -
141D GLU* 3.6 24.0 - - + +
144D VAL* 3.6 26.2 - - + -
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Residues in contact with CYS 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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64D MET* 5.1 1.6 - - + -
81D ALA* 3.4 21.3 - - + +
84D TYR* 3.7 19.6 - - + -
85D LEU* 3.6 34.3 - - + -
88D TYR* 5.6 0.2 - - - -
102D LEU* 3.2 30.1 + - - -
103D GLY* 3.7 8.1 - - - +
105D VAL* 1.3 79.0 - - - +
107D MET* 1.3 65.7 + - - +
109D LEU* 3.3 2.4 + - - -
110D ALA* 2.8 27.2 + - - +
144D VAL* 4.9 7.6 - - - -
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Residues in contact with MET 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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63D TRP* 3.7 23.8 - - + -
64D MET* 3.6 58.8 - - + +
67D VAL* 4.0 16.6 - - + -
68D CYS* 3.8 15.7 - - - -
77D VAL* 4.1 3.0 - - + +
81D ALA* 3.8 12.0 - - + +
103D GLY 3.0 9.3 + - - +
104D ALA* 3.1 11.2 - - - +
106D CYS* 1.3 75.9 - - - +
108D LEU* 1.3 63.3 + - - +
110D ALA* 3.3 1.9 + - - +
111D SER* 2.9 24.9 + - - -
119D LEU* 4.1 12.1 - - + -
124D LEU* 4.0 17.5 - - + -
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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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52A GLY 5.2 0.2 - - - +
104D ALA 2.7 15.9 + - - +
105D VAL* 3.2 9.9 - - - +
107D MET* 1.3 72.6 - - - +
109D LEU* 1.3 59.0 + - - +
111D SER* 3.1 6.0 + - - -
112D LYS* 2.8 50.7 + - + +
119D LEU* 3.1 29.6 - - - +
120D THR* 4.6 0.4 - - - -
121D ILE* 4.2 25.8 - - + -
124D LEU* 3.7 16.0 - - + +
137D LEU* 4.7 13.7 - - + +
141D GLU* 3.7 36.6 - - + +
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Residues in contact with LEU 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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59A VAL* 4.7 9.2 - - + +
84D TYR* 4.0 12.8 - - + -
105D VAL* 2.8 30.4 + - + +
106D CYS* 3.8 5.4 - - - +
108D LEU* 1.3 72.0 - - - +
110D ALA* 1.3 64.3 + - - +
112D LYS* 2.9 18.5 + - + +
113D LEU* 3.0 15.3 + - - +
141D GLU* 3.7 33.2 - - + +
144D VAL* 3.9 30.3 - - + -
145D LEU* 4.0 23.1 - - + -
152D LEU* 4.0 25.0 - - + +
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Residues in contact with ALA 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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77D VAL* 3.5 32.1 - - + +
80D LEU* 3.9 10.7 - - + +
81D ALA* 3.6 13.2 - - + +
84D TYR* 3.4 14.3 - - + -
106D CYS 2.8 21.2 + - - +
107D MET 3.5 3.6 - - - +
109D LEU* 1.3 74.2 - - - +
111D SER* 1.3 61.7 + - - +
113D LEU* 3.3 2.8 + - - +
114D ARG* 3.2 24.3 + - - +
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Residues in contact with SER 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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77D VAL* 3.8 14.5 - - - +
107D MET 2.9 12.5 + - - -
108D LEU 3.4 8.1 - - - -
110D ALA* 1.3 76.2 - - - +
112D LYS* 1.3 63.7 + - - +
113D LEU 3.0 0.2 + - - -
115D GLU* 2.8 49.6 + - - +
118D PRO* 3.1 7.4 - - - +
119D LEU* 3.0 39.5 + - - +
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Residues in contact with LYS 112 (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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53A GLY* 3.6 8.4 - - - -
54A LEU* 2.7 44.1 + - + +
56A ILE* 3.2 27.1 - - + +
59A VAL* 5.3 11.0 - - + -
60A ARG* 3.1 24.0 + - - +
108D LEU* 2.8 40.2 + - + +
109D LEU* 2.9 14.3 + - + +
111D SER* 1.3 73.2 - - - +
113D LEU* 1.3 57.1 + - - +
118D PRO* 3.5 20.0 - - + -
119D LEU 5.0 1.8 - - - -
121D ILE* 5.8 0.4 - - - -
141D GLU* 2.6 31.5 + - - +
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Residues in contact with LEU 113 (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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59A VAL* 4.1 18.2 - - + +
60A ARG* 3.8 29.0 + - + +
63A ALA* 3.9 24.2 - - + -
80D LEU* 4.4 7.9 - - + -
84D TYR* 3.5 10.3 - - - +
109D LEU 3.0 13.7 + - - +
110D ALA 3.7 4.7 - - - +
111D SER 3.0 0.4 - - - -
112D LYS* 1.3 79.1 - - - +
114D ARG* 1.3 64.4 + - + +
115D GLU 3.8 0.9 - - - -
152D LEU* 3.0 40.6 - - + +
153D ALA* 3.7 11.2 - - + +
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Residues in contact with ARG 114 (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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60A ARG* 4.8 0.9 - - - -
67A ARG* 6.2 1.0 - - - +
74D GLU* 3.9 11.8 - - + +
76D GLU* 3.1 43.1 + - + +
77D VAL* 4.8 7.4 - - + -
80D LEU* 3.2 29.3 - - + +
110D ALA 3.2 12.0 + - - +
111D SER 3.1 2.2 + - - -
113D LEU* 1.3 87.2 - - - +
115D GLU* 1.3 64.1 + - - +
153D ALA* 4.6 3.6 - - - +
154D ALA 3.1 30.9 + - - +
156D ILE* 4.7 3.1 - - - +
159D ASP* 2.8 34.1 + - - -
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Residues in contact with GLU 115 (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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60A ARG* 2.6 28.0 + - - +
72D ARG 4.6 1.0 - - - +
73D CYS* 3.3 29.7 - - - +
74D GLU* 3.2 34.4 + - + +
77D VAL* 3.4 17.3 - - + +
111D SER* 2.8 32.0 + - - +
113D LEU 3.8 0.2 - - - -
114D ARG* 1.3 84.1 - - - +
116D THR* 1.3 63.1 + - - +
117D THR 4.3 8.9 - - - +
118D PRO* 3.5 15.0 - - + +
119D LEU* 4.6 1.5 - - - +
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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
------------------------------------------------------------
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