Contacts of the helix formed by residues 103 - 119 (chain A) in PDB entry 1U75
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.2 11.0 + - - -
96A HIS* 4.6 0.2 - - - -
101A TRP 3.6 2.2 + - - -
102A ILE* 1.3 75.3 - - - +
104A SER* 1.3 59.4 + - - +
105A GLY 4.2 0.9 - - - -
106A ASP* 3.1 21.8 + - - +
107A LEU* 3.0 25.8 + - - +
130A ARG 2.6 30.0 + - - -
131A VAL* 4.5 0.4 - - - -
132A ASP* 3.3 22.0 - - - -
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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
----------------------------------------------------------
69A GLY* 4.0 13.5 - - - -
72A ARG* 3.6 17.7 - - - +
89A PHE* 6.0 0.2 - - - -
96A HIS* 3.7 20.5 + - - -
102A ILE 3.9 1.2 + - - -
103A SER* 1.3 68.7 - - - +
105A GLY* 1.3 57.0 + - - +
107A LEU* 3.2 8.0 + - - +
108A PHE* 2.9 60.1 + - - -
132A ASP* 2.9 20.3 + - - -
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.3 2.8 - - - +
66A SER 3.5 23.1 - - - -
67A TYR 4.5 0.8 + - - -
69A GLY* 3.9 9.5 - - - -
103A SER* 3.2 1.4 + - - -
104A SER* 1.3 77.9 - - - +
106A ASP* 1.3 60.0 + - - +
108A PHE* 4.0 4.8 - - - +
109A SER* 2.9 29.3 + - - -
130A ARG* 3.6 15.5 - - - -
132A ASP* 3.8 4.9 + - - -
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Residues in contact with ASP 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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11A GLU* 2.8 27.5 - - - +
102A ILE* 3.9 9.0 - - + -
103A SER* 3.1 20.6 + - - +
105A GLY* 1.3 74.6 - - - +
107A LEU* 1.3 57.6 + - - +
109A SER* 3.1 4.5 + - - -
110A LEU* 3.0 31.9 + - - +
126A TRP* 3.2 16.3 - - + -
128A CYS* 3.7 1.6 - - - +
129A GLY 3.0 21.8 + - - -
130A ARG* 2.7 45.9 + - - +
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Residues in contact with LEU 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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22A VAL* 4.4 9.9 - - + -
26A ILE* 4.1 13.0 - - + +
92A LEU* 3.9 27.3 - - + +
95A ILE* 4.0 27.1 - - + -
96A HIS* 3.6 39.0 - - + +
102A ILE* 4.2 17.4 - - + +
103A SER 3.0 15.5 + - - +
104A SER* 3.7 4.0 - - - +
106A ASP* 1.3 75.8 - - - +
108A PHE* 1.3 70.1 + - + +
110A LEU* 3.3 3.2 + - - +
111A GLY* 2.8 28.6 + - - -
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Residues in contact with PHE 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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46A LEU 4.5 1.7 - - - +
49A LEU* 4.0 17.2 - - + +
50A ALA* 3.8 12.0 + - - +
53A ILE* 3.6 36.3 - - + -
69A GLY* 4.2 9.6 - - - -
71A TYR* 3.8 23.8 - + + -
72A ARG* 4.5 3.4 - - + -
89A PHE* 3.7 39.3 - + - -
92A LEU* 3.9 24.2 - - + +
96A HIS* 6.4 0.7 - + - -
104A SER* 2.9 45.1 + - - +
105A GLY* 4.4 2.9 - - - -
107A LEU* 1.3 86.9 - - + +
109A SER* 1.3 60.8 + - - +
111A GLY* 3.5 6.8 + - - -
112A GLY 3.5 8.0 + - - -
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Residues in contact with SER 109 (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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50A ALA* 4.3 5.4 - - - -
53A ILE* 4.6 8.1 - - - -
66A SER* 5.1 0.7 - - - -
105A GLY 2.9 20.2 + - - -
106A ASP 3.1 3.6 + - - -
108A PHE* 1.3 75.3 - - - +
110A LEU* 1.3 59.0 + - - +
111A GLY 3.1 1.6 - - - -
112A GLY* 3.0 16.1 + - - -
113A VAL* 3.1 15.9 + - - +
126A TRP* 2.9 26.6 + - - -
130A ARG* 3.2 19.4 + - - -
270A LEU* 3.7 24.5 - - - +
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Residues in contact with LEU 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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19A PHE* 4.2 11.0 - - + +
22A VAL* 4.1 32.1 - - + -
23A TYR* 3.8 16.2 - - + +
26A ILE* 4.6 3.4 - - + -
102A ILE* 4.2 7.6 - - + -
106A ASP 3.0 18.0 + - - +
107A LEU* 3.8 4.7 - - - +
109A SER* 1.3 73.8 + - - +
111A GLY* 1.3 57.8 + - - +
113A VAL* 3.2 4.7 + - + -
114A THR* 2.6 51.7 + - - +
126A TRP* 3.9 36.1 - - + +
286A PHE* 3.7 22.0 - - + -
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Residues in contact with GLY 111 (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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26A ILE* 4.2 19.9 - - - +
46A LEU* 3.6 17.4 - - - +
92A LEU* 4.6 9.6 - - - -
107A LEU 2.8 16.6 + - - -
108A PHE 3.8 4.3 - - - -
109A SER 3.1 0.6 - - - -
110A LEU* 1.3 77.8 - - - +
112A GLY* 1.3 55.5 + - - +
114A THR* 3.9 1.6 - - - -
115A ALA* 3.2 27.4 + - - +
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Residues in contact with GLY 112 (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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46A LEU 3.6 20.6 + - - -
47A VAL* 4.2 2.8 - - - +
50A ALA* 3.7 12.3 - - - -
108A PHE 3.5 5.5 + - - -
109A SER 3.0 8.6 + - - -
111A GLY* 1.3 77.0 - - - +
113A VAL* 1.3 61.4 + - - +
115A ALA* 3.7 1.6 - - - +
116A VAL* 3.3 29.1 + - - +
266A PHE* 3.7 9.4 - - - -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.8 1.1 - - + -
109A SER 3.1 12.8 + - - +
110A LEU* 3.2 10.5 + - + +
112A GLY* 1.3 75.2 - - - +
114A THR* 1.3 66.5 + - - +
116A VAL* 3.6 1.2 + - - +
117A GLN* 3.1 37.5 + - - +
124A ILE* 3.6 49.1 - - + +
125A PRO 5.2 0.2 - - - +
126A TRP* 3.8 27.1 - - + -
266A PHE* 4.7 1.8 - - + -
270A LEU* 4.0 10.8 - - + -
286A PHE* 4.5 11.9 - - + -
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Residues in contact with THR 114 (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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23A TYR* 3.2 54.6 - - + +
26A ILE* 3.8 21.3 - - + +
27A ALA* 3.8 17.0 - - + +
30A LEU* 4.5 2.0 - - + -
110A LEU* 2.6 27.1 + - - +
111A GLY 3.9 4.3 - - - -
113A VAL* 1.3 77.1 - - - +
115A ALA* 1.3 56.0 + - - +
117A GLN* 3.3 2.1 + - - +
118A GLU* 2.9 36.8 + - + +
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Residues in contact with ALA 115 (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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30A LEU* 4.3 11.9 - - - +
43A GLY* 3.2 32.8 - - - +
46A LEU* 4.0 7.0 - - + -
47A VAL* 3.6 10.8 - - + -
111A GLY 3.2 19.8 + - - +
112A GLY 3.7 2.5 - - - +
114A THR* 1.3 76.6 - - - +
116A VAL* 1.3 61.9 + - - +
118A GLU* 3.5 1.6 + - - +
119A MET* 3.1 32.1 + - - +
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Residues in contact with VAL 116 (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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47A VAL* 3.8 28.5 - - + -
112A GLY 3.3 16.6 + - - +
113A VAL 4.2 2.5 - - - +
115A ALA* 1.3 79.4 - - - +
117A GLN* 1.3 59.4 + - - +
119A MET* 3.5 10.1 + - - +
121A GLY* 3.1 21.7 + - - -
122A PRO* 4.0 19.3 - - + +
124A ILE* 3.9 28.0 - - + -
198A PHE* 4.1 18.2 - - + +
262A PHE* 4.0 19.5 - - + -
266A PHE* 4.3 2.9 - - + -
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Residues in contact with GLN 117 (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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23A TYR* 2.8 36.2 + - - +
113A VAL* 3.1 23.6 + - - +
114A THR 3.8 0.4 - - - +
116A VAL* 1.3 73.5 - - - +
118A GLU* 1.3 58.0 - - - +
119A MET 3.1 8.1 + - - -
120A GLN* 3.3 11.8 + - - -
121A GLY 3.7 7.8 + - - +
122A PRO 3.6 21.5 - - - +
123A LYS* 3.8 15.7 - - + +
124A ILE* 3.2 32.0 + - + +
285A ILE* 5.4 0.2 - - - -
286A PHE* 3.0 30.0 + - - +
288A THR* 3.9 20.0 - - + +
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Residues in contact with GLU 118 (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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23A TYR* 2.7 31.9 + - - +
27A ALA* 3.7 26.6 - - + +
30A LEU* 4.4 11.4 - - + -
31A ARG* 5.2 1.2 + - - -
114A THR* 2.9 24.9 + - + +
115A ALA 3.9 3.1 - - - +
117A GLN* 1.3 69.7 - - - +
119A MET* 1.3 57.5 + - - +
120A GLN* 3.2 19.5 + - - +
288A THR* 3.4 6.4 - - - -
289A LEU* 3.3 34.1 + - - +
290A GLU 5.0 0.5 + - - -
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Residues in contact with MET 119 (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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30A LEU* 6.1 1.3 - - - -
40A ILE 5.6 0.7 - - - +
43A GLY* 3.5 40.6 - - - +
44A PRO* 3.6 10.3 - - + -
115A ALA* 3.1 21.2 + - - +
116A VAL* 3.7 7.4 - - - +
117A GLN 3.1 1.2 - - - -
118A GLU* 1.3 77.9 - - - +
120A GLN* 1.3 72.6 + - - +
121A GLY 3.2 1.1 + - - -
177A LEU* 3.6 32.3 - - + -
196A ASN* 3.2 33.7 - - - +
197A VAL* 3.7 3.3 - - - +
198A PHE* 2.9 30.3 + - + +
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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
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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