Contacts of the helix formed by residues 91 - 110 (chain A) in PDB entry 1UXI
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 LEU 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ALA* 3.5 23.1 - - + +
81A PRO 4.0 6.5 - - - +
82A ARG* 3.7 38.4 - - + +
86A MET* 4.4 12.6 - - - -
87A SER 4.2 5.2 - - - +
88A ARG* 3.4 17.9 - - - +
89A GLU 3.0 1.0 + - - -
90A ASP* 1.3 76.6 - - - +
92A ILE* 1.3 58.0 + - - +
93A LYS 3.3 3.0 + - - -
94A VAL* 3.5 7.2 + - + +
95A ASN* 2.9 43.6 + - - +
120A ASN* 3.9 10.5 - - + +
121A PRO* 4.2 2.2 - - - -
1310A NAD 3.9 14.8 - - - +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.0 19.5 + - + +
90A ASP 3.3 1.7 - - - +
91A LEU* 1.3 78.1 - - - +
93A LYS* 1.3 63.4 + - + +
96A ALA* 3.0 33.6 + - + +
121A PRO* 3.7 31.8 - - + +
124A ALA* 4.2 9.6 - - + -
125A MET* 4.1 6.3 - - + -
302A THR* 3.4 30.7 - - - +
305A THR* 3.8 28.7 - - + -
306A LEU* 4.1 9.0 - - + +
309A LEU* 3.6 12.1 - - + +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP 4.8 3.3 + - - +
91A LEU 3.3 1.0 - - - -
92A ILE* 1.3 87.0 - - + +
94A VAL* 1.3 72.8 + - + +
96A ALA* 3.5 6.6 + - - +
97A ASP* 2.9 40.9 + - - +
309A LEU* 4.3 26.7 - - + +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 4.3 12.3 - - + -
91A LEU* 3.5 8.1 + - + +
93A LYS* 1.3 84.0 - - + +
95A ASN* 1.3 64.4 + - - +
97A ASP* 3.4 7.6 + - - +
98A ILE* 3.2 44.4 + - + +
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Residues in contact with ASN 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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79A GLY* 3.6 8.2 - - - -
80A ALA* 2.8 51.5 + - - +
91A LEU* 2.9 23.5 + - - +
94A VAL* 1.3 78.5 - - - +
96A ALA* 1.3 58.6 + - - +
98A ILE* 3.7 6.4 - - - +
99A THR* 2.5 40.4 + - - +
119A ASN* 5.0 1.1 - - + -
120A ASN 2.7 20.8 + - - +
125A MET* 3.1 20.4 - - + -
1310A NAD 3.4 6.5 + - - -
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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
----------------------------------------------------------
92A ILE* 3.0 21.9 + - + +
93A LYS 3.8 2.5 - - - +
94A VAL 3.3 0.4 - - - -
95A ASN* 1.3 76.1 - - - +
97A ASP* 1.3 59.4 + - - +
100A ARG* 2.9 33.6 + - - +
125A MET* 3.1 9.5 - - + +
128A LEU* 3.5 19.4 - - + +
306A LEU* 4.3 6.3 - - + -
309A LEU* 3.5 24.2 - - + -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 2.9 43.3 + - - +
94A VAL* 3.4 9.5 + - - +
95A ASN 3.2 0.2 - - - -
96A ALA* 1.3 75.1 - - - +
98A ILE* 1.3 66.9 + - + +
100A ARG* 3.1 11.5 + - - +
101A ALA* 2.9 24.5 + - - +
309A LEU 5.8 0.3 - - - +
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Residues in contact with ILE 98 (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 SER* 3.6 43.3 - - - +
79A GLY 4.4 1.3 - - - +
80A ALA* 4.2 5.6 - - + +
94A VAL* 3.2 35.8 + - + +
95A ASN* 3.7 15.3 - - - +
97A ASP* 1.3 76.3 - - + +
99A THR* 1.3 63.9 + - - +
101A ALA* 3.1 10.0 + - - +
102A CYS* 2.9 27.1 + - - -
119A ASN* 4.7 0.7 - - - +
1310A NAD 3.7 27.8 - - + +
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Residues in contact with THR 99 (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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76A VAL* 5.2 0.9 - - + -
95A ASN 2.5 28.8 + - - -
96A ALA 3.8 2.5 - - - -
98A ILE* 1.3 74.2 - - - +
100A ARG* 1.3 63.2 + - - +
102A CYS* 3.3 5.5 + - - +
103A ILE* 2.9 39.2 + - + +
117A MET* 3.9 26.2 - - + -
119A ASN* 3.2 22.2 + - - +
125A MET* 3.2 25.2 - - - +
128A LEU* 4.0 14.8 - - + -
129A ALA* 4.7 0.4 - - + -
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Residues in contact with ARG 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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96A ALA 2.9 19.8 + - - +
97A ASP* 3.5 8.6 + - - +
99A THR* 1.3 76.6 - - - +
101A ALA* 1.3 58.0 + - - +
103A ILE* 4.8 0.2 - - - -
104A SER* 2.8 39.1 + - - +
128A LEU* 3.7 21.9 - - + +
131A GLU* 4.5 9.7 + - - -
132A VAL* 3.4 37.2 - - + +
306A LEU* 5.8 2.4 - - - +
309A LEU 5.6 4.6 + - - -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP 2.9 12.3 + - - +
98A ILE* 3.2 12.6 - - - +
100A ARG* 1.3 76.8 - - - +
102A CYS* 1.3 60.7 + - - +
104A SER* 2.9 19.0 + - - -
105A GLN* 3.1 29.3 - - - +
1310A NAD 4.4 10.5 - - - +
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Residues in contact with CYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.6 16.6 - - + -
65A TYR* 3.4 16.2 - - - +
76A VAL* 4.6 9.0 - - + -
78A SER* 3.1 28.3 - - - +
98A ILE* 2.9 22.6 + - - +
99A THR 3.9 3.8 - - - +
101A ALA* 1.3 73.6 - - - +
103A ILE* 1.3 60.2 + - + +
105A GLN 3.4 0.7 + - - -
106A ALA* 3.0 32.7 + - - +
1310A NAD 3.4 31.9 - - - -
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 5.8 2.0 - - + -
76A VAL* 4.0 27.1 - - + -
99A THR* 2.9 28.6 + - + +
102A CYS* 1.3 74.8 - - + +
104A SER* 1.3 67.8 + - - +
106A ALA* 4.9 1.3 - - + -
107A ALA* 3.0 34.7 + - + +
115A ILE* 4.1 15.0 - - + -
117A MET* 4.2 0.9 - - + -
129A ALA* 3.7 34.1 - - + +
132A VAL* 3.8 10.8 - - + -
133A SER* 3.6 36.3 - - - +
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Residues in contact with SER 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 ARG* 2.8 31.2 + - - +
101A ALA* 2.9 16.3 + - - -
103A ILE* 1.3 73.0 - - - +
105A GLN* 1.3 61.0 + - - +
108A PRO* 3.0 26.4 - - - +
132A VAL* 3.7 18.7 - - - +
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Residues in contact with GLN 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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65A TYR* 3.4 49.9 + - + +
101A ALA* 3.1 31.3 + - - +
103A ILE 3.1 0.4 - - - -
104A SER* 1.3 82.1 - - - +
106A ALA* 1.3 64.8 + - - +
108A PRO* 3.5 8.1 - - - +
109A LEU* 3.5 20.6 - - - +
1310A NAD 5.6 1.6 + - - -
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Residues in contact with ALA 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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8A ILE* 4.7 7.0 - - + -
65A TYR* 3.8 17.2 - - + -
68A THR* 4.5 12.1 + - - +
74A ILE* 4.0 26.9 - - + +
102A CYS 3.0 17.7 + - - +
103A ILE* 4.9 2.2 - - + -
105A GLN* 1.3 76.3 - - - +
107A ALA* 1.3 66.4 + - - +
109A LEU* 2.9 16.3 + - - +
110A SER* 3.2 12.6 + - - -
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Residues in contact with ALA 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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74A ILE* 4.5 7.1 - - - +
103A ILE* 3.0 22.6 + - + +
106A ALA* 1.3 76.2 - - - +
108A PRO* 1.3 67.1 - - + +
110A SER 3.1 21.4 + - - +
111A PRO* 3.5 1.9 - - - +
115A ILE* 4.5 3.5 - - + +
132A VAL 5.4 0.4 - - - +
133A SER* 3.7 33.0 - - - +
135A PHE* 3.3 24.5 - - + -
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Residues in contact with PRO 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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103A ILE 3.6 0.2 - - - +
104A SER* 3.0 29.2 - - - +
105A GLN 3.5 5.8 - - - +
106A ALA 3.4 2.9 - - - -
107A ALA* 1.3 97.2 - - + +
109A LEU* 1.3 63.8 + - + +
110A SER 3.6 0.2 + - - -
111A PRO* 3.7 11.8 - - + +
135A PHE* 5.6 0.4 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.2 38.4 - - + +
66A ALA* 4.1 9.0 - - - +
68A THR* 4.2 3.4 - - - +
69A ALA* 3.7 22.1 - - + +
70A ASN* 3.0 21.1 + - - +
105A GLN 3.5 18.8 - - - +
106A ALA 2.9 8.3 + - - +
108A PRO* 1.3 84.2 - - + +
110A SER* 1.3 59.1 + - - +
111A PRO* 3.4 6.8 - - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 2.9 17.0 + - - -
70A ASN* 3.3 5.1 + - - +
71A SER* 2.9 40.7 + - - +
74A ILE* 3.9 15.7 - - - +
106A ALA 3.2 3.1 + - - -
107A ALA 3.1 6.1 + - - +
109A LEU* 1.3 78.2 - - - +
111A PRO* 1.3 61.7 - - - +
112A ASN 3.3 2.9 - - - -
113A ALA* 3.3 15.0 + - - +
135A PHE* 3.1 18.2 - - - -
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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