Contacts of the helix formed by residues 104 - 119 (chain B) in PDB entry 2D0U
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 PRO 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 4.2 14.1 - - + +
60B GLU* 4.4 14.1 - - + -
90B TYR* 3.2 45.3 - - + +
102B VAL* 3.4 3.7 - - + +
103B LEU* 1.3 90.4 - - + +
105B ARG* 1.3 56.5 + - - +
106B ASN* 3.1 9.6 - - + +
107B ILE* 2.9 8.5 + - + +
108B ALA 2.7 31.0 + - - -
250B GLU* 4.7 6.1 - - + +
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 4.3 5.0 - - - +
103B LEU 3.4 2.4 + - - -
104B PRO* 1.3 70.3 - - - +
106B ASN* 1.3 78.9 + - - +
107B ILE 3.1 0.2 - - - -
108B ALA* 4.1 0.7 - - - -
109B VAL* 3.1 32.0 + - + +
250B GLU* 3.0 65.0 + - + +
251B GLY* 3.9 20.2 - - - +
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Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 5.2 3.3 + - - -
59B VAL 5.3 1.8 - - - +
60B GLU 5.0 6.2 + - - +
62B LEU* 3.3 31.3 + - + +
63B ASN* 3.6 5.4 - - - +
64B MET* 2.8 43.5 + - - +
65B LEU 4.4 0.5 + - - -
104B PRO* 3.1 7.6 + - + +
105B ARG* 1.3 90.6 - - - +
107B ILE* 1.3 58.5 + - + +
110B PRO* 3.5 18.0 - - - +
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 5.1 3.1 - - - +
59B VAL* 4.3 20.2 - - + +
62B LEU* 4.0 23.3 - - + -
83B LEU* 3.5 42.4 - - + +
86B ILE* 4.7 12.6 - - + -
87B THR* 4.4 9.4 - - - +
103B LEU* 3.5 28.9 - - + -
104B PRO* 2.9 11.2 + - + +
106B ASN* 1.3 77.6 - - + +
108B ALA* 1.3 74.0 + - - +
109B VAL 3.2 1.8 - - - -
110B PRO* 3.0 12.6 - - - +
111B TYR* 3.1 18.5 + - + +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.5 36.1 - - + +
104B PRO 2.7 16.0 + - - +
107B ILE* 1.3 79.9 - - - +
109B VAL* 1.3 56.8 + - - +
111B TYR* 3.7 2.1 - - - +
112B CYS* 2.9 34.9 + - - -
249B TYR* 3.9 16.4 - - + -
250B GLU 3.7 14.4 - - - +
252B PHE* 5.2 1.1 - - - -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 3.9 24.9 - - + -
105B ARG* 3.1 17.9 + - + +
108B ALA* 1.3 74.4 - - - +
110B PRO* 1.3 77.2 - - + +
112B CYS* 3.0 3.8 + - - +
113B GLN* 2.9 55.4 + - + +
250B GLU 4.1 9.2 - - - +
251B GLY* 3.9 26.0 - - - +
252B PHE* 4.5 10.5 - - + +
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Residues in contact with PRO 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 3.8 23.6 - - + -
64B MET* 4.0 7.2 - - + -
65B LEU 3.2 27.8 - - - +
67B ILE* 3.6 16.5 - - + +
83B LEU* 4.2 2.5 - - + -
106B ASN 3.5 18.6 - - - +
107B ILE* 3.0 23.3 - - - +
109B VAL* 1.3 88.2 - - + +
111B TYR* 1.3 56.6 + - - +
113B GLN* 3.1 7.9 + - - +
114B LEU* 2.8 32.9 + - - +
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 3.9 33.1 + - + -
83B LEU* 3.5 30.6 - - + +
84B GLY* 3.4 13.5 - - - -
87B THR* 3.5 28.5 - - + -
103B LEU* 4.5 9.9 - - + -
107B ILE* 3.1 18.6 + - + +
108B ALA* 3.7 3.6 - - - +
109B VAL 3.1 0.6 - - - -
110B PRO* 1.3 80.0 - - - +
112B CYS* 1.3 57.4 + - - +
114B LEU* 3.4 1.5 + - + +
115B SER* 2.9 41.0 + - - -
122B PRO* 3.4 27.1 - - + -
123B ILE* 2.9 38.0 + - - -
124B LEU* 3.3 3.1 + - - -
249B TYR* 4.6 1.3 - + - -
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Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 2.9 21.8 + - - +
111B TYR* 1.3 77.3 - - - +
113B GLN* 1.3 57.8 + - - +
115B SER* 3.6 7.9 - - - -
116B LYS* 3.0 28.2 + - - +
122B PRO* 3.8 5.6 - - - -
249B TYR* 3.2 44.4 - - - -
252B PHE* 3.5 35.0 - - + -
253B TRP* 3.8 17.6 - - + -
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 5.8 1.8 - - - +
65B LEU 5.4 1.0 - - - +
66B SER* 5.5 1.9 + - - -
67B ILE* 3.6 28.2 + - + +
109B VAL* 2.9 41.5 + - - +
110B PRO* 3.6 9.3 - - - +
112B CYS* 1.3 72.8 - - - +
114B LEU* 1.3 65.8 + - - +
116B LYS* 3.4 6.3 + - - +
117B LYS* 3.0 23.6 + - - +
252B PHE* 3.9 18.4 - - + -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.6 16.3 - - + +
70B LEU* 4.1 13.7 - - + -
76B GLN* 3.5 39.3 - - + +
79B ALA* 3.5 31.6 - - + -
80B ARG* 3.5 22.9 - - + +
83B LEU* 4.3 9.9 - - + -
110B PRO 2.8 16.8 + - - +
111B TYR* 3.7 3.8 - - + +
113B GLN* 1.3 77.2 - - - +
115B SER* 1.3 56.9 + - - +
117B LYS* 3.2 9.7 + - + +
118B LEU* 2.9 31.7 + - + +
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Residues in contact with SER 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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80B ARG* 3.7 17.1 + - - +
111B TYR* 2.9 25.0 + - - -
112B CYS* 3.6 7.2 - - - -
114B LEU* 1.3 75.1 - - - +
116B LYS* 1.3 66.4 + - - +
118B LEU* 3.0 2.5 + - - -
119B GLU 2.8 20.4 + - - -
120B LEU 3.0 25.8 + - - -
121B PRO 3.6 3.1 + - - -
122B PRO* 3.2 29.8 - - - +
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Residues in contact with LYS 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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280A GLN* 4.5 18.3 - - + +
112B CYS 3.0 18.4 + - - +
113B GLN* 3.6 7.9 - - - +
115B SER* 1.3 75.3 - - - +
117B LYS* 1.3 65.0 + - - +
119B GLU* 3.1 18.3 + - - +
120B LEU 5.0 0.4 - - - -
252B PHE* 5.0 12.7 - - + -
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Residues in contact with LYS 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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67B ILE* 4.7 21.1 + - + +
68B ASP* 5.7 4.4 + - - +
70B LEU 4.2 15.8 + - - -
71B THR 5.6 0.4 + - - -
76B GLN* 4.0 26.6 - - - +
113B GLN 3.0 14.1 + - - +
114B LEU* 3.3 14.6 - - + +
115B SER 3.1 0.2 - - - -
116B LYS* 1.3 79.6 - - - +
118B LEU* 1.3 60.4 + - + +
119B GLU* 3.3 5.9 + - - +
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Residues in contact with LEU 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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73B HIS* 3.7 26.5 - - + +
76B GLN* 3.4 55.6 - - + +
77B ARG* 4.3 11.7 - - - -
80B ARG* 3.9 21.3 - - + -
114B LEU* 2.9 19.3 + - + +
115B SER 3.9 2.5 - - - +
117B LYS* 1.3 79.3 - - + +
119B GLU* 1.3 72.0 + - - +
120B LEU* 3.4 15.3 + - + +
301B PRO* 3.3 19.6 - - - +
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Residues in contact with GLU 119 (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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280A GLN* 3.7 33.1 + - - +
115B SER 2.8 7.8 + - - -
116B LYS* 3.1 10.7 + - - +
117B LYS 4.4 5.1 - - - +
118B LEU* 1.3 81.4 - - - +
120B LEU* 1.3 56.6 + - - +
297B ARG 4.6 0.3 - - - +
301B PRO* 4.0 28.2 - - + +
304B ARG* 3.0 29.9 + - - +
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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
------------------------------------------------------------
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