Contacts of the helix formed by residues 58 - 71 (chain B) in PDB entry 2NYM
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 VAL 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 3.2 28.3 - - + +
57B GLU* 1.3 76.0 - - - +
59B LYS* 1.3 62.5 + - + +
60B ARG 3.4 0.9 - - - -
61B ALA* 3.7 10.1 + - - +
62B ALA* 3.5 15.6 + - - +
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Residues in contact with LYS 59 (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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41B VAL 5.5 1.3 - - - +
42B LEU* 2.9 38.2 + - + +
45B PHE* 3.4 29.8 - - + +
46B VAL* 4.5 2.8 - - - +
57B GLU 2.6 13.1 + - - +
58B VAL* 1.3 74.3 - - + +
60B ARG* 1.3 53.1 + - - +
61B ALA 2.7 15.8 + - - -
62B ALA* 3.1 15.0 + - - -
63B LEU* 3.3 32.6 + - + +
88B MSE 4.6 1.6 - - - -
92B ASN* 2.8 28.4 + - - -
123B HIS* 3.5 36.2 - - + +
127B VAL* 4.9 1.3 - - - +
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.4 44.6 + - + +
58B VAL 3.4 0.8 - - - -
59B LYS* 1.3 77.1 - - - +
61B ALA* 1.3 59.7 + - - +
63B LEU* 4.6 1.3 - - - -
64B SER* 3.1 28.4 + - - -
122B PRO* 5.1 8.3 - - + +
123B HIS* 4.5 14.7 - - + +
126B LEU* 4.1 19.5 - - + +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 5.6 2.7 - - - +
58B VAL* 3.7 11.1 + - - +
59B LYS 2.7 1.6 + - - -
60B ARG* 1.3 81.8 - - - +
62B ALA* 1.3 54.6 + - - +
63B LEU 2.6 17.4 + - - -
64B SER* 2.8 20.8 + - - +
65B GLU* 2.8 14.9 + - + +
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Residues in contact with ALA 62 (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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38B GLN* 4.6 11.5 - - + +
41B VAL* 5.5 3.6 - - + -
42B LEU* 4.1 17.5 - - + +
58B VAL* 3.5 6.2 + - + +
59B LYS* 3.1 17.7 + - - +
61B ALA* 1.3 77.5 - - - +
63B LEU* 1.3 57.1 + - - +
65B GLU* 3.4 17.6 - - - +
66B MSE 3.2 31.8 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.3 29.6 - - + -
59B LYS* 3.3 26.9 + - + +
60B ARG* 5.9 0.4 - - - -
61B ALA 2.6 5.1 + - - -
62B ALA* 1.3 73.1 - - - +
64B SER* 1.3 52.1 + - - +
65B GLU 2.6 16.1 + - - -
66B MSE 2.9 22.6 + - - +
67B VAL* 2.9 21.2 + - + +
88B MSE 3.7 15.0 - - + -
123B HIS* 4.0 6.5 - - + +
126B LEU* 3.9 28.5 - - + -
127B VAL* 3.6 31.2 - - + +
130B PHE* 5.1 10.0 - - + +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 3.1 31.2 + - - -
61B ALA* 2.8 16.6 + - - +
63B LEU* 1.3 73.1 - - - +
65B GLU* 1.3 54.9 + - - +
67B VAL* 3.7 13.2 - - - +
68B GLU* 3.3 37.2 + - - +
126B LEU* 4.8 13.1 - - - +
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Residues in contact with GLU 65 (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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38B GLN* 5.1 10.7 - - - +
61B ALA 2.8 15.3 + - - +
62B ALA* 3.4 16.1 - - - +
63B LEU 2.6 1.0 + - - -
64B SER* 1.3 77.6 - - - +
66B MSE 1.3 58.0 + - + +
67B VAL 2.6 13.5 + - - -
68B GLU* 3.2 4.3 + - - +
69B TYR* 3.0 29.4 + - + +
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Residues in contact with MSE 66 (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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35B LYS* 4.1 23.8 - - + -
38B GLN* 4.6 8.5 - - + +
39B CYS* 3.6 41.3 - - + -
62B ALA 3.2 16.6 - - - +
63B LEU* 2.9 18.9 + - - +
65B GLU* 1.3 81.4 - - + +
67B VAL* 1.3 57.6 + - - +
69B TYR* 3.9 13.9 - - + -
70B ILE* 3.2 33.9 - - + +
82B TYR* 5.0 8.3 - - + +
85B VAL* 5.6 1.3 - - + -
88B MSE 6.3 0.9 - - - +
130B PHE* 3.9 41.5 - - + -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 2.9 27.1 - - + +
64B SER* 3.7 13.0 - - - +
65B GLU 2.6 1.0 + - - -
66B MSE 1.3 78.2 - - - +
68B GLU* 1.3 63.0 + - + +
69B TYR 2.6 14.2 + - - -
70B ILE* 2.9 3.0 + - - +
71B THR* 2.9 39.1 + - - +
126B LEU* 5.4 5.6 - - + +
129B GLU* 5.1 15.9 - - + -
130B PHE* 4.3 26.7 - - + +
133B ARG* 5.3 9.0 - - + +
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Residues in contact with GLU 68 (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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64B SER* 3.3 23.0 - - - +
65B GLU* 3.2 5.5 + - - +
67B VAL* 1.3 83.9 - - + +
69B TYR* 1.3 55.7 + - - +
71B THR* 4.6 0.9 - - - -
72B HIS* 3.8 43.1 + - + +
74B ARG* 3.5 19.2 + - - +
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Residues in contact with TYR 69 (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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31B LEU* 3.5 27.7 - - + +
35B LYS* 5.5 11.3 - - + +
65B GLU* 3.0 22.6 + - + +
66B MSE 3.9 11.4 - - + -
67B VAL 2.6 5.7 + - - -
68B GLU* 1.3 76.0 - - - +
70B ILE* 1.3 74.3 + - + +
71B THR 3.5 0.4 - - - -
74B ARG* 3.2 23.7 - - + +
75B ASN* 2.9 54.2 + - - -
78B THR* 4.3 17.9 + - + +
82B TYR* 5.7 0.7 - - - -
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Residues in contact with ILE 70 (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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66B MSE 3.2 24.7 + - + +
67B VAL* 2.9 2.5 + - - +
69B TYR* 1.3 94.9 - - + +
71B THR* 1.3 65.6 + - - +
73B ASN 5.3 0.4 - - - -
74B ARG 5.5 0.2 - - - -
75B ASN* 4.8 13.9 - - + +
78B THR* 5.5 10.1 - - + +
82B TYR* 5.9 1.6 - - - +
130B PHE* 3.4 27.6 - - + -
133B ARG 4.1 18.8 - - - +
134B PHE* 5.4 7.2 - - + -
137B SER* 4.3 9.8 + - - +
140B PHE* 3.6 36.8 - - + -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 2.9 26.2 + - + +
68B GLU* 4.6 2.0 - - - -
70B ILE* 1.3 81.5 - - - +
72B HIS* 1.3 67.1 + - + +
73B ASN* 2.5 22.7 + - - -
75B ASN 5.5 0.2 - - - +
133B ARG* 3.0 56.5 + - - +
137B SER* 5.7 1.1 - - - -
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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