Contacts of the helix formed by residues 77 - 95 (chain B) in PDB entry 5UNG
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 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 1.4 82.0 - - + +
78B VAL* 1.4 64.3 + - - +
79B SER* 3.6 5.8 - - - +
80B SER* 3.5 18.8 - - - +
81B ILE* 3.4 20.1 + - - +
157B PRO* 5.2 9.1 - - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 1.4 70.4 - - - +
79B SER* 1.4 64.7 + - - +
81B ILE* 3.4 18.5 + - - +
82B TYR* 3.5 23.0 - - + +
141B ASP* 4.4 16.4 - - - +
151B LEU 5.5 6.3 - - - +
152B SER* 6.1 3.6 - - - -
154B ARG 6.1 1.3 - - - +
157B PRO* 3.7 32.5 - - + +
159B GLN* 4.3 17.7 - - - +
160B ALA* 3.8 18.0 - - + +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 4.6 5.4 - - - +
78B VAL* 1.4 76.8 - - - +
80B SER* 1.4 66.4 + - - +
82B TYR* 3.1 25.9 + - - +
83B ILE* 3.2 18.7 + - - +
138B MET* 4.0 15.1 - - - +
141B ASP* 3.7 18.1 + - - -
326B GLN* 6.0 2.3 - - - +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.4 15.6 - - - -
73B LYS* 3.4 24.7 + - - +
76B LYS 3.3 21.9 + - - -
77B LYS* 3.5 15.4 + - - +
78B VAL 3.3 1.0 - - - -
79B SER* 1.4 78.0 + - - +
81B ILE* 1.4 61.7 + - - +
83B ILE* 3.4 13.3 + - - +
84B PHE 3.3 18.0 + - - -
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.7 22.0 - - + -
75B PRO* 3.3 29.4 - - + +
77B LYS 3.4 15.5 - - - +
78B VAL* 3.6 9.9 - - - +
79B SER 3.3 0.8 - - - -
80B SER* 1.4 74.8 - - - +
82B TYR* 1.3 57.2 + - + +
84B PHE* 3.6 3.3 + - - +
85B ASN* 2.8 49.9 + - - +
157B PRO* 6.6 0.2 - - + -
160B ALA* 5.1 13.9 - - + +
164B VAL* 3.7 20.2 - - + -
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.5 31.7 - - + +
79B SER* 3.1 14.2 + - - +
81B ILE* 1.3 74.9 - - + +
83B ILE* 1.4 55.1 + - - +
85B ASN* 3.8 4.7 - - - +
86B LEU* 2.9 36.4 + - - +
134B PHE* 3.7 27.9 - + + +
137B CYS* 4.4 13.9 - - + -
138B MET* 3.8 23.3 - - + -
141B ASP* 4.2 23.5 + - + -
159B GLN* 5.1 1.0 - - - +
160B ALA* 3.8 14.5 + - + +
163B ILE* 3.6 47.4 - - + +
164B VAL* 3.9 16.4 - - + -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.8 12.3 - - + +
69B PHE* 6.1 0.4 - - + -
73B LYS* 5.5 6.7 - - - +
79B SER* 3.2 16.3 + - - +
80B SER* 3.5 15.0 - - - +
81B ILE 3.4 0.2 - - - -
82B TYR* 1.4 76.9 - - - +
84B PHE* 1.4 55.5 + - - +
86B LEU* 3.5 7.0 + - + +
87B ALA* 3.0 27.8 + - - +
138B MET* 3.8 26.0 - - + -
318B TYR* 3.7 37.2 - - + +
319B CYS* 3.8 31.0 - - + +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 5.1 3.1 - - - -
66B VAL* 3.8 39.9 - - + -
69B PHE* 3.5 58.8 - + + -
70B CYS* 4.4 9.2 - - - -
80B SER 3.3 3.0 + - - +
81B ILE* 3.9 6.1 - - - +
82B TYR 3.4 0.2 - - - -
83B ILE* 1.4 76.9 - - - +
85B ASN* 1.3 71.5 + - - +
87B ALA* 3.2 6.9 + - - +
88B VAL* 2.9 47.5 + - + +
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Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 2.8 39.0 + - - +
82B TYR 3.8 4.0 - - - +
83B ILE 3.4 0.2 - - - -
84B PHE* 1.3 82.1 - - - +
86B LEU* 1.4 59.9 + - - +
88B VAL* 3.5 7.2 + - - +
89B ALA* 3.0 28.4 + - - +
134B PHE* 3.7 21.9 - - + -
164B VAL* 3.5 26.5 - - - +
168B TRP* 2.9 31.3 + - - -
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Residues in contact with LEU 86 (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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82B TYR 2.9 19.5 + - - +
83B ILE* 3.7 6.3 - - - +
85B ASN* 1.4 73.9 - - - +
87B ALA* 1.4 54.5 + - - +
89B ALA* 3.4 4.0 + - - +
90B ASP* 2.8 57.9 + - - +
131B SER* 3.3 37.7 - - - +
134B PHE* 4.2 11.1 - - + -
135B ILE* 3.8 10.1 - - + +
138B MET* 5.1 6.3 - - + -
314B ASN* 3.8 13.2 - - + +
318B TYR* 3.8 40.6 - - + -
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Residues in contact with ALA 87 (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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62B ASN* 3.5 19.4 - - - +
65B VAL* 3.8 27.6 - - + -
66B VAL* 3.9 15.8 - - + +
83B ILE 3.0 17.9 + - - +
84B PHE* 3.4 6.7 - - - +
86B LEU* 1.4 73.7 - - - +
88B VAL* 1.4 58.1 + - - +
90B ASP* 4.5 0.7 - - - -
91B LEU* 2.9 30.8 + - - +
315B PRO* 6.1 0.4 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.9 12.1 - - + -
84B PHE* 2.9 52.2 + - + +
85B ASN* 3.9 7.0 - - - +
86B LEU 3.4 0.2 - - - -
87B ALA* 1.4 71.7 - - - +
89B ALA* 1.4 60.3 + - - +
91B LEU* 3.4 7.2 + - + +
92B LEU* 3.0 51.0 + - + +
168B TRP* 4.7 11.9 - - + -
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Residues in contact with ALA 89 (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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85B ASN 3.0 18.4 + - - +
86B LEU* 3.4 5.4 + - - +
88B VAL* 1.4 74.9 - - - +
90B ASP* 1.4 60.9 + - - +
93B LEU* 3.2 23.9 + - - +
127B ASN* 3.5 20.8 - - - +
130B ALA* 3.8 31.4 - - + +
131B SER* 3.8 14.6 - - - +
134B PHE* 5.1 0.2 - - + -
168B TRP* 4.0 6.0 - - + -
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Residues in contact with ASP 90 (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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62B ASN* 3.5 19.4 - - - +
86B LEU* 2.8 30.3 + - - +
87B ALA* 4.5 0.2 - - - -
89B ALA* 1.4 74.0 - - - +
91B LEU* 1.4 58.5 + - - +
93B LEU* 3.2 4.0 + - - +
94B LEU* 2.9 36.5 + - - +
131B SER* 2.7 26.6 + - - -
311B SER* 2.9 29.3 + - - -
314B ASN* 3.1 31.8 + - - +
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Residues in contact with LEU 91 (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 PHE* 3.4 54.5 - - + +
62B ASN* 3.8 15.8 - - + +
63B ILE* 3.8 27.1 - - + +
66B VAL* 4.7 14.8 - - + -
87B ALA 2.9 20.1 + - - +
88B VAL* 3.4 6.5 + - + +
90B ASP* 1.4 74.6 - - - +
92B LEU* 1.3 62.1 + - + +
94B LEU* 3.5 5.3 + - - +
95B ALA* 3.0 28.3 + - - +
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Residues in contact with LEU 92 (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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88B VAL* 3.0 37.7 + - + +
89B ALA 4.3 0.2 - - - +
91B LEU* 1.3 79.1 - - + +
93B LEU* 1.4 62.3 + - - +
95B ALA* 3.4 16.2 - - + +
96B THR* 3.6 4.9 - - - +
123B PHE* 3.4 41.0 - - + -
127B ASN* 3.5 31.2 - - - +
168B TRP* 5.1 4.0 - - + -
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Residues in contact with LEU 93 (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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89B ALA 3.2 17.6 + - - +
90B ASP* 3.2 4.6 + - - +
92B LEU* 1.4 73.7 - - - +
94B LEU* 1.4 61.9 + - - +
96B THR* 2.7 27.8 + - - -
123B PHE 5.8 0.2 - - - -
124B LEU* 3.5 43.5 - - + +
127B ASN* 4.0 8.3 - - + +
128B MET* 3.8 31.2 - - + +
131B SER* 4.7 5.8 - - - -
269B TRP* 5.5 2.0 - - + -
307B GLY 5.2 5.8 - - - +
308B PHE* 3.3 24.9 - - + -
311B SER* 3.4 23.1 - - - +
1201B 8ES 4.4 4.7 - - + -
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Residues in contact with LEU 94 (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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54B ILE* 4.1 6.3 - - + +
55B PHE* 3.2 24.8 - - - +
58B GLY* 3.6 17.5 - - - +
59B PHE* 4.8 3.8 - - + +
62B ASN* 3.5 26.9 - - - +
90B ASP 2.9 21.6 + - - +
91B LEU* 4.0 5.6 - - - +
93B LEU* 1.4 70.1 - - - +
95B ALA* 1.4 55.7 + - - +
96B THR 3.1 4.9 - - - -
97B LEU* 3.2 42.3 + - + +
308B PHE* 3.4 29.2 - - + +
311B SER* 3.8 14.8 - - - +
312B CYS* 3.8 13.9 - - - -
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Residues in contact with ALA 95 (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 PHE* 4.1 11.3 - - - -
59B PHE* 4.4 13.2 - - + -
91B LEU 3.0 18.1 + - - +
92B LEU* 3.4 16.8 - - + +
93B LEU 3.2 0.2 - - - -
94B LEU* 1.4 76.2 - - - +
96B THR* 1.4 56.9 + - + +
97B LEU 3.4 0.2 - - - -
98B PRO* 3.4 15.4 - - - +
99B LEU* 4.8 4.7 - - - +
123B PHE* 5.4 2.5 - - + -
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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