Contacts of the helix formed by residues 104 - 120 (chain B) in PDB entry 3N9Y
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 LYS 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLU* 2.8 45.2 + - + +
83B LEU* 6.5 1.8 - - + -
102B LEU 5.6 0.9 - - - +
103B LYS* 1.3 75.4 - - - +
105B SER* 1.3 85.8 + - - +
107B ALA* 3.4 8.5 + - - +
108B TRP* 3.1 15.1 + - - -
421B ARG* 4.4 4.7 - - - +
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Residues in contact with SER 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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78B ASN* 3.5 40.5 + - - +
80B GLU* 4.9 1.6 + - - -
104B LYS* 1.3 95.4 - - - +
106B ALA* 1.3 71.1 + - - +
107B ALA 4.7 0.2 - - - -
108B TRP* 3.1 10.9 + - - +
109B LYS 3.1 9.5 + - - -
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Residues in contact with ALA 106 (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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78B ASN* 3.7 6.1 - - - +
105B SER* 1.3 84.9 + - - +
107B ALA* 1.3 57.3 + - - +
109B LYS* 3.3 8.6 + - - +
110B LYS* 3.0 28.8 + - - +
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Residues in contact with ALA 107 (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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103B LYS* 3.7 27.0 + - + +
104B LYS 3.4 6.7 + - - +
105B SER* 3.2 1.0 - - - -
106B ALA* 1.3 79.5 - - - +
108B TRP* 1.3 61.8 + - - +
110B LYS* 3.7 9.0 + - - +
111B ASP* 3.5 16.1 + - - +
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Residues in contact with TRP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO 4.1 8.5 - - - -
78B ASN* 3.9 26.2 - - + -
79B PRO* 4.2 6.1 - - + -
100B VAL* 3.1 39.9 - - + +
103B LYS* 3.7 9.3 - - - +
104B LYS* 3.1 28.6 + - - +
105B SER 3.4 7.6 - - - +
107B ALA* 1.3 74.6 - - - +
109B LYS* 1.3 90.4 + - + +
111B ASP* 3.3 4.5 + - - +
112B ARG* 2.9 43.7 + - + +
420B VAL* 3.6 36.1 - - + -
421B ARG* 3.2 43.1 - - + +
601B HEM 2.9 19.8 + - - -
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 4.1 14.0 - - - +
78B ASN* 3.7 26.2 - - - +
105B SER 3.1 6.8 + - - +
106B ALA* 3.3 11.2 + - - +
108B TRP* 1.3 93.7 - - + +
110B LYS* 1.3 56.0 + - - +
112B ARG* 4.4 2.5 - - + -
113B VAL* 3.0 51.1 + - + +
420B VAL* 5.3 4.7 - - - -
45D ALA* 3.0 31.5 + - - +
47D GLU* 4.2 9.5 + - - +
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Residues in contact with LYS 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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106B ALA 3.0 15.7 + - - +
107B ALA* 3.8 9.4 - - - +
108B TRP 3.3 0.2 - - - -
109B LYS* 1.3 76.9 - - - +
111B ASP* 1.3 66.3 + - - +
113B VAL* 3.5 9.4 - - - +
114B ALA* 3.3 22.3 + - - +
271B LYS* 4.4 26.0 + - + -
272B MET* 5.2 4.8 - - + +
276B ASP* 5.3 8.0 + - - +
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Residues in contact with ASP 111 (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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100B VAL* 4.0 14.8 + - + -
103B LYS* 2.7 36.7 + - + +
107B ALA 3.5 6.5 + - - +
108B TRP 3.3 7.7 + - - +
110B LYS* 1.3 80.9 - - - +
112B ARG* 1.3 60.0 + - - +
114B ALA 3.3 1.2 + - - -
115B LEU* 2.8 30.2 + - - +
272B MET* 3.3 31.8 - - + +
276B ASP* 3.6 12.2 - - - +
280B ASN* 2.8 23.2 + - - +
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Residues in contact with ARG 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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100B VAL* 4.1 8.3 - - + +
108B TRP* 2.9 40.7 + - + +
109B LYS* 3.3 7.1 + - + +
111B ASP* 1.3 76.5 - - - +
113B VAL* 1.3 54.9 + - + +
115B LEU* 3.1 3.0 + - - +
116B ASN* 2.7 70.8 + - - +
120B MET* 4.1 7.1 - - - +
420B VAL 3.4 22.2 + - - +
421B ARG* 3.8 3.2 - - - +
422B GLN* 2.8 40.0 + - - +
423B CYS 3.9 3.8 + - - -
424B LEU* 3.5 26.6 - - - +
601B HEM 2.9 39.0 + - - +
51D ALA* 5.0 1.8 - - - +
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Residues in contact with VAL 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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109B LYS* 3.0 41.7 + - + +
110B LYS* 3.5 11.4 - - + +
112B ARG* 1.3 77.6 - - + +
114B ALA* 1.3 64.5 + - + +
116B ASN* 3.6 8.7 + - - +
117B GLN* 3.1 28.6 + - - +
45D ALA 4.5 6.5 - - - +
46D CYS* 4.6 6.5 - - - +
47D GLU* 3.6 43.3 - - + +
49D THR* 5.3 0.2 - - - +
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Residues in contact with ALA 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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110B LYS 3.3 13.9 + - - +
111B ASP 3.3 4.4 + - - +
113B VAL* 1.3 84.2 - - + +
115B LEU* 1.3 63.1 + - - +
117B GLN* 3.5 17.7 + - - +
118B GLU* 3.9 3.3 + - - +
266B LEU* 4.2 11.3 - - - +
270B SER* 4.0 11.3 + - - +
271B LYS* 5.1 8.1 - - + +
272B MET* 3.9 27.1 - - + +
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Residues in contact with LEU 115 (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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100B VAL* 4.2 7.6 - - + -
111B ASP 2.8 25.1 + - - +
112B ARG 3.7 2.5 - - - +
114B ALA* 1.3 69.8 - - - +
116B ASN* 1.3 65.2 + - - +
117B GLN 3.1 1.8 - - - -
118B GLU* 3.0 5.4 + - + +
119B VAL* 2.9 30.9 + - + +
266B LEU* 4.0 28.7 - - + -
272B MET* 3.6 14.1 - - + -
280B ASN* 3.5 39.7 - - + +
284B MET* 4.5 15.9 - - - -
424B LEU* 3.7 29.8 - - + -
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Residues in contact with ASN 116 (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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112B ARG* 2.7 57.4 + - - +
113B VAL* 3.9 8.7 - - - +
115B LEU* 1.3 72.8 - - - +
117B GLN* 1.3 56.8 + - - +
120B MET* 2.9 28.1 + - - +
121B ALA 2.9 27.9 + - - -
420B VAL 4.9 2.2 + - - -
424B LEU* 3.5 3.2 - - - +
46D CYS* 4.0 15.1 + - - +
49D THR* 3.6 29.5 + - + +
51D ALA* 3.8 11.3 - - - +
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Residues in contact with GLN 117 (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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113B VAL* 3.1 19.5 + - - +
114B ALA* 3.6 11.0 - - - +
115B LEU 3.1 1.0 - - - -
116B ASN* 1.3 76.2 - - - +
118B GLU* 1.3 70.7 + - + +
121B ALA* 3.9 11.3 - - - +
124B ALA* 3.4 15.9 - - - +
46D CYS 5.3 0.2 + - - -
47D GLU* 4.0 27.7 + - - +
49D THR* 3.7 16.8 - - - +
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Residues in contact with GLU 118 (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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114B ALA 4.5 2.9 - - - +
115B LEU* 3.0 7.5 + - + +
117B GLN* 1.3 89.3 - - + +
119B VAL* 1.3 61.2 + - + +
124B ALA* 3.5 13.1 - - - +
128B PHE* 3.4 21.0 - - - -
259B TYR* 4.8 2.8 + - - -
262B ILE* 4.0 21.7 - - + +
265B ARG* 3.0 58.5 + - + +
266B LEU* 3.7 26.0 - - + +
269B ASP* 5.0 8.3 - - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 2.9 16.9 + - + +
118B GLU* 1.3 82.8 - - + +
120B MET* 1.3 61.6 + - + +
125B THR* 3.3 17.2 - - - +
128B PHE* 3.9 9.1 - - - -
262B ILE* 3.6 22.9 - - + -
284B MET* 3.5 31.2 - - + -
424B LEU* 3.2 43.7 - - + +
425B GLY* 5.1 0.2 - - - -
427B ARG* 3.9 8.1 - - - +
428B ILE* 4.3 11.6 + - + +
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Residues in contact with MET 120 (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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112B ARG* 4.1 6.3 - - - +
116B ASN* 2.9 34.9 + - + +
119B VAL* 1.3 83.9 - - + +
121B ALA* 1.3 66.0 + - - +
122B PRO* 3.3 4.2 - - - +
125B THR* 3.7 3.5 - - - +
422B GLN* 4.0 19.1 - - - +
423B CYS 3.8 17.5 - - - +
424B LEU* 3.3 25.8 - - + +
426B ARG* 4.4 4.7 - - + -
427B ARG* 3.7 46.4 + - + +
49D THR 3.5 8.9 - - - +
50D LEU* 5.4 0.6 - - - +
51D ALA* 3.8 31.6 - - + -
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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