Contacts of the helix formed by residues 90 - 110 (chain A) in PDB entry 5U5S
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 HIS 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASN* 3.9 23.3 - - + -
87A PRO* 3.3 18.2 + - + +
88A PRO 3.4 2.4 + - - +
89A ASP* 1.3 79.9 - - - +
91A ASP* 1.3 78.3 + - + +
92A VAL* 3.4 19.8 - - + +
93A VAL* 3.0 17.9 - - + +
94A ALA* 3.5 6.8 + - - +
286B ILE* 3.7 31.0 - - + +
287B ALY 2.9 30.4 + - - -
289B PHE* 4.1 13.7 - - + -
290B LEU* 3.9 13.4 - - + +
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 1.3 80.4 + - - +
92A VAL* 1.3 59.1 + - - +
94A ALA* 3.1 8.2 + - - +
95A MET* 2.9 49.9 + - + +
289B PHE* 3.8 25.3 - - + +
290B LEU* 4.8 5.4 - - - +
291B GLN* 4.9 5.8 + - - -
292B SER 5.8 0.5 + - - -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 3.5 31.4 - - + -
29A PHE* 4.2 5.8 - - + -
82A CYS* 4.6 4.2 - - + +
86A ASN* 3.3 34.3 - - - +
90A HIS* 3.4 14.1 - - + +
91A ASP* 1.3 75.1 - - - +
93A VAL* 1.3 58.3 + - - +
95A MET* 4.0 6.1 - - - +
96A ALA* 3.0 27.0 + - - +
287B ALY 4.1 19.1 - - + +
289B PHE* 3.7 28.7 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A CYS* 4.4 3.4 - - - +
83A TYR* 3.6 27.3 - - + -
86A ASN* 3.2 38.6 - - + +
87A PRO 3.5 8.3 - - - +
88A PRO* 3.3 31.9 - - + +
90A HIS 3.0 21.3 - - - +
92A VAL* 1.3 77.6 - - - +
94A ALA* 1.3 60.9 + - + +
96A ALA* 3.2 1.6 + - - +
97A ARG* 2.8 39.5 + - + +
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Residues in contact with ALA 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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90A HIS 3.9 8.1 - - - +
91A ASP* 3.1 10.4 + - - +
93A VAL* 1.3 82.5 - - + +
95A MET* 1.3 64.7 + - + +
97A ARG* 3.4 11.1 + - - +
98A LYS* 3.2 23.2 + - - +
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Residues in contact with MET 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 4.7 1.6 - - - +
25A TYR* 3.6 38.5 - - + +
27A TRP* 4.1 23.6 - - + -
28A PRO* 3.6 26.2 - - + -
29A PHE* 3.6 10.6 - - + -
91A ASP* 2.9 44.1 + - + +
92A VAL* 4.0 6.5 - - - +
94A ALA* 1.3 74.8 - - + +
96A ALA* 1.3 61.1 + - - +
98A LYS* 3.4 5.2 + - - +
99A LEU* 2.9 31.5 + - - +
289B PHE* 4.5 7.0 - - + -
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Residues in contact with ALA 96 (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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29A PHE* 3.5 21.5 - - + -
79A PHE* 3.9 14.1 - - + +
82A CYS* 4.4 9.4 - - + -
83A TYR* 3.5 20.4 - - + +
92A VAL 3.0 20.4 + - - +
93A VAL* 3.2 5.8 + - - +
95A MET* 1.3 74.8 - - - +
97A ARG* 1.3 55.9 + - - +
99A LEU 3.7 0.7 - - - -
100A GLN* 2.7 35.7 + - - +
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Residues in contact with ARG 97 (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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83A TYR* 3.1 22.4 - - + +
93A VAL* 2.8 31.5 + - - +
94A ALA* 3.7 9.6 - - - +
95A MET 3.3 0.2 - - - -
96A ALA* 1.3 76.6 - - - +
98A LYS* 1.3 62.7 + - - +
100A GLN* 3.3 8.0 + - - +
101A ASP* 3.1 20.3 + - - +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.5 53.7 + - + -
94A ALA 3.2 14.2 + - - +
95A MET* 3.9 4.9 - - - +
97A ARG* 1.3 76.2 - - - +
99A LEU* 1.3 61.6 + - - +
101A ASP* 2.9 29.1 + - + +
102A VAL* 3.3 7.0 + - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.0 20.4 - - + +
22A HIS* 3.9 12.1 - - + -
25A TYR* 3.5 40.2 - - + +
26A ALA* 3.4 15.3 - - + -
29A PHE* 3.3 33.2 - - + -
53A LEU* 4.9 2.5 - - + -
79A PHE* 3.7 19.8 - - + -
95A MET 2.9 13.2 + - - +
98A LYS* 1.3 76.0 - - - +
100A GLN* 1.3 59.7 + - - +
102A VAL* 3.0 31.7 - - + +
103A PHE* 3.1 14.4 + - - +
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Residues in contact with GLN 100 (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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79A PHE* 4.3 23.2 - - + +
83A TYR* 3.0 36.2 + - - -
96A ALA 2.7 20.1 + - - +
97A ARG* 3.3 7.4 - - - +
98A LYS 3.1 0.2 - - - -
99A LEU* 1.3 71.0 - - - +
101A ASP* 1.3 60.4 + - - +
103A PHE* 4.0 5.1 - - + +
104A GLU* 2.8 42.8 + - + +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG 3.1 10.9 + - - +
98A LYS* 2.9 15.4 + - + +
100A GLN* 1.3 76.8 - - - +
102A VAL* 1.3 65.9 + - - +
104A GLU* 3.2 5.9 + - - +
105A PHE* 2.9 53.3 + - - -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.1 40.2 - - - +
17A LEU* 3.7 5.4 - - + -
22A HIS* 3.5 16.4 - - + -
25A TYR* 5.5 0.7 - - + -
98A LYS 3.3 2.6 + - - +
99A LEU* 3.0 48.7 - - + +
101A ASP* 1.3 78.5 + - - +
103A PHE* 1.3 55.1 - - - +
105A PHE* 3.2 6.3 + - - +
106A ARG* 2.9 36.2 + - + +
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.0 15.3 - - + -
17A LEU* 3.9 18.4 - - + -
71A PHE* 3.8 13.9 - + - -
72A ALA* 4.1 15.7 - - + -
75A VAL* 3.3 39.3 - - + -
76A ARG* 4.3 20.9 - - + -
79A PHE* 3.6 23.3 - + + -
99A LEU 3.1 16.0 + - - +
100A GLN* 4.3 8.7 - - + -
102A VAL* 1.3 78.9 - - - +
104A GLU* 1.3 68.4 + - - +
106A ARG* 3.2 8.3 + - - +
107A TYR* 2.9 34.1 + + + +
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Residues in contact with GLU 104 (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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100A GLN* 2.8 30.6 + - + +
101A ASP* 3.3 7.6 - - - +
102A VAL 3.2 0.2 - - - -
103A PHE* 1.3 84.7 - - + +
105A PHE* 1.3 72.0 + - + +
107A TYR* 3.4 6.4 + - - +
108A ALA* 2.8 34.2 + - + +
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Residues in contact with PHE 105 (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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101A ASP* 2.9 53.8 + - - +
102A VAL* 3.9 4.0 - - - +
104A GLU* 1.3 85.9 - - + +
106A ARG* 1.3 61.6 + - - +
108A ALA* 3.6 12.1 - - + -
109A LYS* 2.9 51.6 + - - +
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Residues in contact with ARG 106 (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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9A HIS* 4.5 3.5 + - - -
13A ILE* 3.6 34.3 - - + +
16A GLU* 2.6 50.1 + - - +
21A LYS* 5.3 7.7 - - - +
102A VAL* 2.9 26.3 + - - +
103A PHE* 3.4 7.4 - - - +
105A PHE* 1.3 78.4 - - - +
107A TYR* 1.3 57.6 + - - +
109A LYS* 3.4 15.0 + - - +
110A MET* 3.0 25.3 + - - +
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Residues in contact with TYR 107 (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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13A ILE* 4.0 8.7 - - + +
68A ALA* 3.4 31.8 - - + +
69A GLN* 3.0 34.9 + - - +
71A PHE* 4.8 6.3 - + - -
72A ALA* 3.6 18.4 - - + -
76A ARG* 5.3 7.9 - - - -
103A PHE* 2.9 31.3 + + + +
104A GLU* 3.8 6.1 - - - +
106A ARG* 1.3 74.4 - - - +
108A ALA* 1.3 60.7 + - - +
110A MET* 3.1 46.3 + - - +
112A ASP* 4.9 8.6 + - + +
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Residues in contact with ALA 108 (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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104A GLU* 2.8 26.0 + - + +
105A PHE* 3.6 19.5 - - + +
106A ARG 3.2 0.2 - - - -
107A TYR* 1.3 81.2 - - - +
109A LYS* 1.3 63.0 + - + +
110A MET 3.7 3.6 + - - +
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A HIS* 4.9 4.5 - - - +
105A PHE* 2.9 43.8 + - - +
106A ARG* 3.9 15.2 - - - +
108A ALA* 1.3 77.2 - - + +
110A MET* 1.3 65.3 + - - +
111A PRO* 3.3 10.0 - - - +
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Residues in contact with MET 110 (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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6A GLN* 3.7 22.9 - - + +
9A HIS* 3.6 36.1 + - + -
13A ILE* 4.4 4.5 - - + -
68A ALA* 3.3 31.0 - - + -
106A ARG 3.0 13.5 + - - +
107A TYR* 3.1 46.9 + - + +
108A ALA 4.0 3.6 - - - +
109A LYS* 1.3 75.5 - - - +
111A PRO* 1.3 83.0 - - + +
112A ASP* 3.8 13.6 + - + +
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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
------------------------------------------------------------
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