Contacts of the helix formed by residues 78 - 95 (chain A) in PDB entry 5UNF
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LYS* 1.4 75.1 - - - +
79A SER* 1.4 65.8 + - - +
80A SER 3.3 1.1 - - - -
81A ILE* 3.1 19.9 + - - +
82A TYR* 3.3 26.9 - - + +
141A ASP* 4.7 2.7 - - - +
157A PRO* 4.2 28.7 - - + +
159A GLN* 3.5 28.3 - - + +
160A ALA* 3.8 22.7 - - + -
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.7 25.3 + - - -
78A VAL* 1.4 77.4 - - - +
80A SER* 1.4 62.3 + - - +
82A TYR* 3.3 17.3 + - - +
83A ILE* 3.2 26.7 + - - +
138A MET* 3.9 11.2 - - - +
141A ASP* 3.4 21.8 + - - -
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.4 13.8 - - - -
73A LYS* 3.6 33.3 + - - +
76A LYS 3.6 12.8 - - - -
77A LYS* 3.5 22.7 + - - +
78A VAL 3.3 0.8 - - - +
79A SER* 1.4 75.9 + - - +
81A ILE* 1.4 63.8 + - - +
83A ILE* 3.4 14.2 + - - +
84A PHE 3.2 17.5 + - - -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.7 23.6 - - + -
75A PRO* 3.4 27.8 - - + +
76A LYS 4.2 0.7 - - - +
77A LYS 3.2 19.3 - - - +
78A VAL* 3.1 12.5 + - - +
80A SER* 1.4 74.2 - - - +
82A TYR* 1.4 60.3 + - + +
84A PHE* 3.4 4.5 + - + +
85A ASN* 2.8 45.0 + - - +
160A ALA* 4.7 14.1 - - + -
164A VAL* 3.8 17.7 - - + -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 3.3 44.9 - - + +
79A SER* 3.3 14.0 + - - +
81A ILE* 1.4 75.3 - - + +
83A ILE* 1.4 53.1 + - - +
85A ASN* 3.4 4.7 + - - +
86A LEU* 2.8 36.2 + - - +
134A PHE* 4.1 23.9 - + + +
137A CYS* 4.0 20.9 - - + -
138A MET* 3.7 23.3 - - + -
141A ASP* 4.1 20.4 - - + -
159A GLN* 4.2 6.1 + - - -
160A ALA* 4.3 7.6 - - + -
163A ILE* 3.4 47.4 - - + +
164A VAL* 4.9 10.5 - - + -
116B MET* 4.6 1.6 - - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.8 14.6 - - + -
69A PHE* 6.4 0.7 - - + -
79A SER* 3.2 15.6 + - - +
80A SER* 3.4 15.5 - - - +
81A ILE 3.3 0.2 - - - -
82A TYR* 1.4 75.3 - - - +
84A PHE* 1.4 51.8 + - - +
86A LEU* 3.3 9.2 + - + +
87A ALA* 2.8 33.1 + - - +
138A MET* 3.6 25.4 - - + -
318A TYR* 3.6 37.0 - - + +
319A CYS* 3.8 29.4 - - + +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 5.4 2.0 - - - -
66A VAL* 3.7 37.2 - - + -
69A PHE* 3.6 41.5 - + + -
70A CYS* 4.1 15.9 - - - -
80A SER 3.2 10.3 + - - +
81A ILE* 3.4 8.7 + - + +
83A ILE* 1.4 77.9 - - - +
85A ASN* 1.3 66.7 + - - +
87A ALA* 3.1 7.8 + - - +
88A VAL* 2.8 54.7 + - + +
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Residues in contact with ASN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 2.8 33.4 + - - +
82A TYR 3.8 1.8 - - - +
84A PHE* 1.3 83.8 - - - +
86A LEU* 1.4 56.1 + - - +
88A VAL* 3.8 7.2 - - - +
89A ALA* 3.0 29.5 + - - +
134A PHE* 3.5 27.6 - - + -
164A VAL* 3.4 37.6 - - - +
168A TRP* 3.1 25.6 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR 2.8 17.7 + - - +
83A ILE* 3.5 8.5 - - + +
84A PHE 3.2 0.2 - - - -
85A ASN* 1.4 75.3 - - - +
87A ALA* 1.4 52.5 + - - +
89A ALA* 3.4 4.4 + - - +
90A ASP* 2.8 45.9 + - - +
131A SER* 3.3 34.8 - - - +
134A PHE* 4.1 12.7 - - + +
135A ILE* 3.7 7.0 - - + +
138A MET* 4.8 11.2 - - + -
314A ASN* 3.6 26.9 - - + +
318A TYR* 4.0 34.1 - - + -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASN* 3.9 19.6 - - - +
65A VAL* 3.9 22.2 - - + -
66A VAL* 3.8 20.9 - - + -
83A ILE 2.8 16.5 + - - +
84A PHE* 3.1 7.4 + - - +
86A LEU* 1.4 73.0 - - - +
88A VAL* 1.4 54.3 + - - +
90A ASP* 3.8 1.8 - - - +
91A LEU* 2.8 37.5 + - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.8 8.7 - - + -
84A PHE* 2.8 50.6 + - + +
85A ASN* 3.8 7.6 - - - +
87A ALA* 1.4 71.6 - - - +
89A ALA* 1.4 57.8 + - - +
91A LEU* 3.3 9.0 + - + +
92A LEU* 2.9 51.0 + - + +
168A TRP* 4.3 14.8 - - + -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN 3.0 18.7 + - - +
86A LEU* 3.6 4.5 - - - +
88A VAL* 1.4 76.3 - - - +
90A ASP* 1.4 56.2 + - - +
93A LEU* 3.1 28.9 + - - +
127A ASN* 3.4 21.0 - - - +
130A ALA* 3.8 18.4 - - + +
131A SER* 3.7 28.5 - - - +
168A TRP* 4.0 5.2 - - + -
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASN* 3.6 22.2 - - - +
86A LEU* 2.8 32.5 + - - +
87A ALA* 3.8 2.9 - - - +
89A ALA* 1.4 69.6 - - - +
91A LEU* 1.4 60.4 + - - +
93A LEU* 3.2 3.0 + - - +
94A LEU* 3.0 37.2 + - - +
131A SER* 2.7 26.3 + - - -
311A SER* 3.0 24.7 + - - -
314A ASN* 3.1 31.6 + - - +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.6 57.3 - - + +
62A ASN* 3.8 16.5 - - + +
63A ILE* 4.0 16.8 - - + -
66A VAL* 4.3 20.9 - - + -
87A ALA 2.8 21.4 + - - +
88A VAL* 3.5 8.7 - - + +
90A ASP* 1.4 74.0 - - - +
92A LEU* 1.4 60.9 + - + +
94A LEU* 3.5 4.1 + - - +
95A ALA* 3.1 26.3 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 2.9 35.9 + - + +
91A LEU* 1.4 80.6 - - + +
93A LEU* 1.4 63.2 + - - +
95A ALA* 3.4 20.2 + - + +
96A THR* 3.8 4.3 - - - +
123A PHE* 3.5 37.4 - - + -
127A ASN* 3.5 31.9 - - - +
168A TRP* 5.2 2.7 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 3.1 19.0 + - - +
90A ASP 3.2 4.2 + - - +
92A LEU* 1.4 76.0 - - - +
94A LEU* 1.4 60.1 - - - +
96A THR* 2.7 28.5 + - - -
123A PHE 5.9 0.2 - - - -
124A LEU* 3.4 46.7 - - + +
127A ASN* 4.1 7.8 - - + +
128A MET* 3.8 28.9 - - + +
131A SER* 4.8 7.6 - - - -
269A TRP* 5.3 4.5 - - + -
307A GLY 5.1 3.1 - - - +
308A PHE* 3.4 26.9 - - + -
311A SER* 3.5 22.7 - - - +
1501A 8ES 4.7 2.7 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 4.2 12.8 - - + +
55A PHE* 3.0 32.1 - - - +
58A GLY* 3.4 34.8 - - - +
59A PHE* 4.6 5.4 - - + -
62A ASN* 3.4 16.6 - - - +
90A ASP 3.0 16.9 + - - +
91A LEU* 3.9 4.7 - - - +
93A LEU* 1.4 73.4 - - - +
95A ALA* 1.4 58.6 + - - +
96A THR 3.2 3.1 + - - -
97A LEU* 3.3 33.0 + - + +
308A PHE* 3.4 31.6 - - + +
311A SER* 3.8 13.0 - - - +
312A CYS* 4.4 1.6 - - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.9 11.6 - - + -
59A PHE* 4.3 11.2 - - + -
91A LEU 3.1 14.3 + - - +
92A LEU* 3.4 22.2 - - + +
93A LEU 3.2 0.4 - - - -
94A LEU* 1.4 76.1 - - - +
96A THR* 1.4 57.1 + - + +
97A LEU 3.5 0.4 - - - -
98A PRO* 3.4 14.6 - - - +
99A LEU* 5.4 2.3 + - - +
123A PHE* 5.4 2.7 - - + -
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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