Contacts of the helix formed by residues 59 - 77 (chain B) in PDB entry 4IYM
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 ASN 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ALA 3.7 3.2 + - - -
58B THR* 1.3 78.5 - - - +
60B PRO* 1.3 73.9 - - + +
61B GLN* 2.9 16.0 + - - +
62B ARG* 2.8 46.1 + - - +
63B ARG* 3.0 17.3 + - - +
65B ARG* 5.8 0.2 - - - +
124C GLY 3.5 14.8 - - - +
125C ALA 3.7 16.6 + - - +
126C GLY* 4.7 7.8 - - - -
127C PRO* 6.0 1.0 - - - +
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Residues in contact with PRO 60 (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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58B THR 3.7 0.2 - - - -
59B ASN* 1.3 89.9 - - + +
61B GLN* 1.3 57.1 + - + +
63B ARG* 3.4 29.3 + - + +
64B ALA* 2.9 28.8 + - - +
113B ILE* 3.6 8.1 - - + +
114B PRO* 3.7 32.1 - - + -
117B GLN* 5.7 3.6 - - + +
122C THR* 4.6 18.2 - - + -
123C GLU 4.7 4.0 - - - +
124C GLY 3.4 14.4 - - - +
125C ALA* 4.5 4.0 - - - +
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN* 2.9 10.9 + - - +
60B PRO* 1.3 78.6 - - + +
62B ARG* 1.3 59.1 + - - +
64B ALA* 3.4 5.8 - - - +
65B ARG* 3.0 57.9 + - - +
68B MSE 5.0 0.7 - - - +
114B PRO* 4.1 21.3 - - + -
125C ALA 4.8 8.1 - - - +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 5.6 0.2 - - - -
58B THR* 3.6 28.7 + - + +
59B ASN* 2.8 36.6 + - - +
61B GLN* 1.3 73.7 - - - +
63B ARG* 1.3 65.8 + - - +
65B ARG* 3.2 33.2 + - - +
66B VAL* 3.5 13.7 + - - +
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Residues in contact with ARG 63 (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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55B TRP* 3.6 56.8 - - + +
56B ALA 3.9 10.3 + - - -
58B THR* 2.8 38.4 + - - +
59B ASN 3.0 15.3 + - - +
60B PRO* 3.7 29.6 - - - +
62B ARG* 1.3 74.1 - - - +
64B ALA* 1.3 63.4 + - - +
66B VAL* 3.1 20.8 + - - +
67B PHE* 3.7 11.6 + - - -
113B ILE* 4.2 7.0 - - + +
117B GLN* 2.9 32.5 + - - +
163B ALA* 2.8 28.3 + - - +
164B CYS 3.9 3.0 + - - -
165B GLY* 3.8 11.1 - - - +
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Residues in contact with ALA 64 (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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60B PRO 2.9 17.1 + - - +
61B GLN* 3.4 10.5 - - - +
63B ARG* 1.3 77.0 - - - +
65B ARG* 1.3 56.8 + - - +
67B PHE* 3.0 24.1 + - - +
68B MSE 3.0 21.2 + - + +
111B ILE* 3.3 35.0 - - - +
113B ILE* 4.1 9.3 - - + +
114B PRO* 4.4 2.7 - - + -
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Residues in contact with ARG 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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59B ASN* 5.8 0.2 - - - +
61B GLN* 3.0 43.4 + - - +
62B ARG* 3.2 32.6 + - - +
64B ALA* 1.3 72.0 - - - +
66B VAL* 1.3 64.9 + - + +
68B MSE 3.3 26.8 - - + +
69B LYS* 3.0 23.4 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 3.9 18.6 - - + -
62B ARG 3.5 7.4 + - - +
63B ARG 3.1 11.8 + - - +
65B ARG* 1.3 77.5 - - - +
67B PHE* 1.3 59.5 + - + +
69B LYS* 3.2 1.7 + - - +
70B PHE* 2.9 25.8 + - - +
187B MSE 4.2 12.6 - - + -
190B ALA* 3.6 20.1 - - + +
191B GLY* 3.7 22.4 - - - +
192B LEU* 4.0 34.8 - - + +
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Residues in contact with PHE 67 (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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55B TRP* 4.9 2.5 - + - -
63B ARG 3.7 16.2 - - - -
64B ALA* 3.0 10.7 + - - +
66B VAL* 1.3 77.4 - - + +
68B MSE 1.3 58.2 + - - +
70B PHE* 3.6 4.4 - + - +
71B VAL* 3.0 35.0 + - - +
107B CYS* 3.8 30.7 - - + +
110B VAL* 3.7 17.0 - - + -
111B ILE* 4.2 6.7 - - + +
158B PHE* 4.7 1.8 - + - -
159B ALA* 3.3 39.5 - - + -
162B ILE* 3.8 15.5 - - + -
163B ALA* 3.7 27.4 - - + -
187B MSE 3.6 33.4 - - + -
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Residues in contact with MSE 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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61B GLN 5.0 0.7 - - - +
64B ALA* 3.0 12.7 + - + +
65B ARG* 3.3 48.5 - - + +
67B PHE* 1.3 73.8 - - - +
69B LYS* 1.3 67.8 + - - +
71B VAL* 3.6 4.6 + - - +
72B GLN* 3.3 18.9 + - - +
111B ILE* 3.4 39.6 - - + +
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Residues in contact with LYS 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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65B ARG 3.0 10.6 + - - +
66B VAL 3.6 7.4 - - - +
68B MSE 1.3 82.5 - - - +
70B PHE* 1.3 63.9 + - - +
72B GLN* 3.1 21.4 + - + +
73B LEU* 2.9 41.8 + - + +
189B GLU* 4.9 4.6 + - - +
190B ALA* 3.8 27.8 - - - +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL 2.9 17.0 + - - +
67B PHE* 3.3 8.0 + + - +
69B LYS* 1.3 76.3 - - - +
71B VAL* 1.3 56.2 + - - +
73B LEU* 3.1 6.3 + - + +
74B LEU* 2.9 65.8 + - + +
107B CYS* 3.7 29.4 - - + -
155B MSE 4.0 5.4 - - - -
158B PHE* 4.3 10.1 - + - -
183B LEU* 3.5 34.1 - - + -
186B LEU* 3.7 26.2 - - + -
187B MSE 3.4 36.1 - - + -
190B ALA* 3.7 7.5 - - + +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE 3.0 20.6 + - - +
68B MSE 3.9 6.5 - - - +
69B LYS 3.2 0.2 - - - -
70B PHE* 1.3 75.3 - - - +
72B GLN* 1.3 61.2 + - - +
74B LEU* 3.3 10.8 + - + +
75B ASN* 2.9 38.5 + - - +
104B LEU* 3.9 27.7 - - + +
107B CYS* 3.6 26.7 - - + -
108B GLU* 4.1 21.8 - - + +
111B ILE* 4.9 4.0 - - + -
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Residues in contact with GLN 72 (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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68B MSE 3.3 9.8 + - - +
69B LYS* 3.1 25.6 + - + +
71B VAL* 1.3 79.8 - - - +
73B LEU* 1.3 57.1 + - - +
75B ASN* 3.3 17.8 + - - +
76B ASP* 2.9 65.6 + - - +
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Residues in contact with LEU 73 (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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69B LYS* 2.9 30.7 + - + +
70B PHE* 3.1 8.2 + - - +
72B GLN* 1.3 72.5 - - - +
74B LEU* 1.3 62.0 + - - +
76B ASP* 3.4 12.2 + - + +
77B ASN* 2.8 42.6 + - - +
186B LEU* 3.5 38.1 - - + +
189B GLU* 3.5 35.0 - - + +
190B ALA* 3.5 26.9 - - + +
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Residues in contact with LEU 74 (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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70B PHE* 2.9 60.9 + - + +
71B VAL* 3.5 9.2 - - - +
72B GLN 3.3 0.2 - - - -
73B LEU* 1.3 73.9 - - - +
75B ASN* 1.3 64.3 + - - +
77B ASN 3.3 2.1 + - - -
78B MSE 3.0 29.8 + - - +
81B LEU* 4.0 15.8 - - + +
100B ILE* 4.8 8.1 - - + -
104B LEU* 3.9 32.1 - - + -
107B CYS* 4.7 0.9 - - - -
155B MSE 3.7 18.8 - - + -
183B LEU* 3.8 19.5 - - + -
186B LEU* 4.4 4.7 - - + -
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Residues in contact with ASN 75 (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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71B VAL* 2.9 35.4 + - - +
72B GLN* 3.3 23.4 + - - +
74B LEU* 1.3 76.1 - - - +
76B ASP* 1.3 63.0 + - - +
77B ASN 3.3 0.7 + - - -
78B MSE 3.3 27.0 + - - +
104B LEU* 3.6 15.8 - - - +
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Residues in contact with ASP 76 (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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72B GLN* 2.9 49.7 + - - +
73B LEU* 3.7 15.5 - - + +
74B LEU 3.3 0.2 - - - -
75B ASN* 1.3 76.1 - - - +
77B ASN* 1.3 67.7 + - - +
78B MSE 3.4 1.0 + - - -
79B ASN 5.3 0.5 + - - -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 2.8 33.7 + - - +
74B LEU 3.5 3.6 - - - +
76B ASP* 1.3 85.6 - - - +
78B MSE 1.3 63.8 + - - +
79B ASN 3.4 2.5 - - - -
80B GLU* 3.3 20.9 + - - +
81B LEU* 3.0 33.7 + - + +
182B ARG* 3.3 19.2 + - - +
186B LEU* 3.6 25.3 - - + +
189B GLU* 5.4 0.6 + - - -
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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
------------------------------------------------------------
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