Contacts of the helix formed by residues 103 - 122 (chain E) in PDB entry 1NVI
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 HIS 103 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ALA* 3.6 8.4 - - - +
101E SER* 3.5 20.6 + - - +
102E ALA* 1.3 97.5 + - + +
104E ARG* 1.3 64.6 + - - +
105E SER* 3.4 7.6 + - - +
106E SER* 3.6 8.2 + - - +
107E ALA 3.7 0.5 + - - -
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Residues in contact with ARG 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ALA* 3.7 16.2 - - + +
32E VAL* 5.9 0.2 - - - -
103E HIS* 1.3 73.7 - - - +
105E SER* 1.3 71.5 + - - +
107E ALA* 3.2 3.0 + - - +
108E PHE* 3.0 45.9 + - + -
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Residues in contact with SER 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E HIS* 3.4 4.9 - - - +
104E ARG* 1.3 86.3 - - - +
106E SER* 1.3 62.0 + - - +
108E PHE* 3.5 5.6 + - - +
109E GLU* 3.0 50.8 + - - +
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E TRP* 3.6 32.3 - - - -
75E PRO* 3.7 13.2 - - - +
76E LEU* 4.6 1.3 - - - -
101E SER* 3.2 24.9 - - - -
103E HIS* 3.6 5.7 + - - +
104E ARG 3.3 0.6 - - - -
105E SER* 1.3 82.3 + - - +
107E ALA* 1.3 58.6 + - - +
109E GLU* 4.0 0.4 - - - +
110E ALA* 2.9 34.5 + - - +
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Residues in contact with ALA 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ALA* 4.2 13.5 - - + +
32E VAL* 3.5 29.6 - - + +
99E VAL* 4.1 24.7 - - - +
101E SER* 3.9 14.7 - - - +
103E HIS 3.7 4.9 + - - +
104E ARG 3.2 7.0 + - - +
106E SER* 1.3 79.2 - - - +
108E PHE* 1.3 57.0 + - - +
111E GLY* 3.0 27.0 + - - -
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Residues in contact with PHE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 4.0 28.7 - - + +
104E ARG* 3.0 46.8 + - + +
105E SER* 3.9 5.8 - - - +
107E ALA* 1.3 76.0 - - - +
109E GLU* 1.3 64.4 + - + +
111E GLY* 3.5 0.9 + - - -
112E GLN* 3.2 25.7 + - - +
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Residues in contact with GLU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E TRP* 2.9 37.4 + - + +
105E SER* 3.0 36.0 + - - +
106E SER 4.0 0.2 - - - +
108E PHE* 1.3 80.0 - - + +
110E ALA* 1.3 59.0 + - - +
112E GLN* 3.2 3.2 + - - +
113E PHE* 2.9 28.1 + - - +
150E TRP* 3.5 23.2 - - + -
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Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ALA* 4.7 2.7 - - + -
74E TRP* 3.7 28.4 - - + -
76E LEU* 3.8 29.2 - - + -
99E VAL* 4.0 5.6 - - + -
106E SER 2.9 19.7 + - - +
109E GLU* 1.3 73.8 - - - +
111E GLY* 1.3 65.2 + - - +
113E PHE* 3.6 0.5 - - - +
114E ILE* 2.9 31.3 + - - +
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Residues in contact with GLY 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 5.0 8.7 - - - -
34E PHE* 5.5 4.3 - - - +
97E VAL* 4.1 10.4 - - - +
99E VAL* 4.0 15.6 - - - +
107E ALA 3.0 19.5 + - - -
108E PHE 4.0 1.1 - - - -
110E ALA* 1.3 75.6 - - - +
112E GLN* 1.3 61.0 + - - +
114E ILE* 3.5 3.1 + - - +
115E MET* 3.3 25.1 + - - +
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Residues in contact with GLN 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PHE 3.2 18.8 + - - +
109E GLU* 3.8 3.3 - - - +
111E GLY* 1.3 73.8 - - - +
113E PHE* 1.3 60.7 + - - +
115E MET* 3.3 7.4 + - + +
116E ASP* 2.9 48.9 + - - +
149E ARG* 3.7 23.1 + - - +
150E TRP* 4.1 13.4 - - + -
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Residues in contact with PHE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ILE* 3.9 11.0 - - + -
69E GLU* 3.7 16.4 - - + -
70E ALA* 3.9 28.7 - - + -
73E ARG* 3.7 16.2 - - - -
74E TRP* 3.5 26.2 - + + -
109E GLU 2.9 16.0 + - - +
110E ALA 3.6 2.9 - - - +
112E GLN* 1.3 76.7 - - - +
114E ILE* 1.3 66.2 + - + +
116E ASP* 3.2 1.9 + - - +
117E TYR* 3.0 73.1 + + - +
150E TRP* 3.5 41.1 - + + +
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Residues in contact with ILE 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU* 6.4 0.7 - - + -
66E ILE* 3.9 23.9 - - + +
67E VAL* 4.3 7.4 - - + -
70E ALA* 4.0 26.2 - - + -
76E LEU* 5.1 1.8 - - + -
79E VAL* 4.2 16.6 - - + -
81E VAL* 4.0 15.3 - - + -
97E VAL* 3.9 24.5 - - + -
99E VAL* 3.8 24.2 - - + -
110E ALA* 2.9 21.8 + - + +
111E GLY 3.9 4.0 - - - +
113E PHE* 1.3 76.2 - - + +
115E MET* 1.3 57.9 + - - +
117E TYR 3.8 0.3 - - - -
118E LEU* 2.9 30.1 + - + +
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Residues in contact with MET 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLY* 4.0 21.8 - - - +
34E PHE* 3.6 46.4 - - + -
95E VAL* 4.0 16.4 - - + -
97E VAL* 3.7 24.7 - - + -
111E GLY 3.3 12.6 + - - +
112E GLN* 3.3 10.2 + - + +
113E PHE 3.2 0.6 - - - -
114E ILE* 1.3 77.2 - - - +
116E ASP* 1.3 62.6 + - - +
118E LEU* 3.7 8.4 - - + +
119E LYS* 3.0 48.9 + - + +
151E SO4 6.0 0.9 - - - +
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Residues in contact with ASP 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLN* 2.9 27.9 + - - +
113E PHE 3.2 3.8 + - - +
115E MET* 1.3 77.6 - - - +
117E TYR* 1.3 62.5 + - + +
119E LYS* 3.5 6.0 + - - +
120E THR* 3.2 29.0 + - - +
143E ASP* 4.5 2.8 - - - +
146E ALA* 3.3 29.3 - - + +
147E ALA* 3.8 10.2 - - - +
149E ARG* 2.8 27.2 + - - -
150E TRP* 2.9 16.0 + - + +
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Residues in contact with TYR 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ILE* 3.8 28.0 - - + -
69E GLU* 4.6 8.5 - - + -
73E ARG* 3.9 13.7 + - - -
113E PHE* 3.0 60.3 + + - +
116E ASP* 1.3 76.7 - - + +
118E LEU* 1.3 55.6 + - - +
120E THR* 3.1 4.7 + - - -
121E ARG* 2.7 88.2 + - - +
147E ALA* 3.3 37.1 + - + -
148E LYS* 5.8 0.2 - - - -
150E TRP* 4.5 3.5 + + - -
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Residues in contact with LEU 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLY* 4.2 4.4 - - - -
81D GLY* 3.7 34.8 - - - +
63E LEU* 3.7 25.4 - - + -
66E ILE* 3.8 14.7 - - + +
81E VAL* 4.1 14.1 - - + -
83E HIS* 3.9 13.2 - - + -
95E VAL* 4.0 21.3 - - + -
97E VAL* 5.0 1.6 - - + -
114E ILE* 2.9 21.6 + - + +
115E MET* 3.3 13.9 + - + +
117E TYR* 1.3 75.8 - - - +
119E LYS* 1.3 66.9 + - + +
122E ALA* 3.2 32.8 + - + +
124E PHE* 5.0 0.4 - - + -
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Residues in contact with LYS 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D VAL* 3.5 21.5 - - - +
79D THR* 5.1 2.1 - - - +
80D GLY 2.9 31.8 + - - +
81D GLY* 3.1 25.3 + - - -
115E MET* 3.0 35.0 + - + +
116E ASP* 3.7 8.5 - - - +
117E TYR 3.2 0.2 - - - -
118E LEU* 1.3 81.2 - - + +
120E THR* 1.3 59.5 + - - +
126E LYS* 4.6 3.6 - - - +
140E ARG* 6.3 0.4 - - - +
143E ASP* 3.8 36.1 - - + +
151E SO4 3.3 26.1 + - - +
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Residues in contact with THR 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 5.3 4.9 - - - +
59D LEU* 4.4 7.1 - - - +
78D VAL* 3.5 17.6 - - - +
116E ASP 3.2 15.6 + - - +
117E TYR* 3.3 6.8 + - - -
119E LYS* 1.3 81.2 - - - +
121E ARG* 1.3 69.2 + - - +
143E ASP* 3.4 36.3 - - + +
144E GLN* 3.8 29.5 + - - +
147E ALA* 3.6 15.8 - - + +
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Residues in contact with ARG 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D LEU* 3.8 28.5 - - + +
78D VAL* 4.7 2.6 - - - +
58E MET* 4.8 1.9 - - - +
62E ALA* 4.0 9.3 - - + +
66E ILE* 4.5 11.0 - - + -
69E GLU* 5.9 1.2 - - - +
117E TYR* 2.7 71.5 + - - +
120E THR* 1.3 89.0 + - - +
122E ALA* 1.3 59.6 + - - +
123E PRO* 3.5 8.7 - - - +
147E ALA* 6.0 0.8 - - - +
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Residues in contact with ALA 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D VAL* 3.2 18.1 - - - +
80D GLY 5.1 0.7 + - - -
59E THR 5.4 0.7 - - - +
62E ALA* 4.3 4.7 - - + -
63E LEU* 4.1 21.8 - - + -
66E ILE* 4.8 2.2 - - + +
117E TYR 4.0 0.6 + - - -
118E LEU* 3.2 22.5 + - + +
121E ARG* 1.3 77.6 - - - +
123E PRO* 1.3 65.7 - - + +
124E PHE* 2.9 34.9 + - + +
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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
------------------------------------------------------------
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