Contacts of the helix formed by residues 96 - 113 (chain A) in PDB entry 1UWV
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A GLU* 2.7 44.7 + - - -
77A GLU* 3.5 29.5 - - - +
95A ALA* 1.3 76.9 - - - +
97A VAL* 1.3 58.0 + - - +
98A ASP* 3.6 6.0 + - - +
99A LEU* 3.0 18.3 + - - +
100A GLN* 3.0 24.9 + - - +
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Residues in contact with VAL 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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77A GLU* 5.0 0.4 + - - -
95A ALA 3.6 0.6 + - - -
96A SER* 1.3 69.6 - - - +
98A ASP* 1.3 69.2 + - - +
100A GLN* 3.3 13.2 + - - +
101A GLN* 3.0 47.9 + - - +
124A PRO* 3.7 32.8 - - + -
125A TRP* 5.9 0.7 - - - +
415A ASP* 4.5 4.7 - - - +
418A PRO* 5.5 2.9 - - + -
419A HIS* 4.3 15.3 - - + +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 4.6 4.9 - - - +
96A SER* 3.3 9.9 + - - +
97A VAL* 1.3 79.1 - - - +
99A LEU* 1.3 53.3 + - - +
101A GLN* 3.6 12.7 - - - +
102A ARG* 2.8 51.7 + - - +
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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
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24A LEU* 4.2 8.5 - - + -
45A LEU* 4.3 9.2 - - + -
46A PRO* 4.0 34.8 - - + -
73A SER* 5.2 0.9 - - - +
75A GLU* 3.8 26.9 - - + -
95A ALA* 3.9 18.2 - - + -
96A SER* 3.0 19.5 + - - +
98A ASP* 1.3 76.2 - - - +
100A GLN* 1.3 66.1 + - - +
102A ARG* 3.8 23.9 - - - +
103A SER* 2.8 44.5 + - - +
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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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92A GLN* 2.9 44.0 + - - +
95A ALA* 2.9 26.1 + - + +
96A SER 3.0 15.4 + - - +
97A VAL* 3.7 12.7 - - - +
99A LEU* 1.3 76.5 - - - +
101A GLN* 1.3 60.6 + - + +
103A SER* 3.4 3.0 + - - -
104A LYS* 3.1 48.2 + - - +
415A ASP* 5.0 5.9 - - - +
418A PRO* 3.9 6.4 - - - +
419A HIS* 2.9 47.4 + - - -
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Residues in contact with GLN 101 (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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97A VAL* 3.0 35.7 + - - +
98A ASP* 3.6 11.0 - - - +
100A GLN* 1.3 76.9 - - + +
102A ARG* 1.3 55.1 + - - +
104A LYS* 3.6 4.2 + - - +
105A SER* 2.8 38.8 + - - -
119A VAL* 3.8 29.0 - - + +
121A ALA* 3.6 24.5 - - - +
413A MSE 4.9 4.7 - - - +
415A ASP* 3.0 31.5 + - + +
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Residues in contact with ARG 102 (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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75A GLU* 3.0 34.5 + - - +
98A ASP* 2.8 26.4 + - - +
99A LEU* 3.8 34.4 - - - +
101A GLN* 1.3 73.2 - - - +
103A SER* 1.3 56.0 + - - +
105A SER* 3.9 4.6 - - - -
106A ALA* 3.0 31.2 + - + +
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Residues in contact with SER 103 (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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24A LEU* 3.8 36.2 + - - +
25A ASP 5.3 2.5 - - - -
26A SER* 6.3 2.0 - - - -
46A PRO* 5.3 0.3 - - - +
92A GLN* 5.9 0.2 - - - -
99A LEU* 2.8 38.1 + - - +
100A GLN* 3.8 3.8 - - - -
102A ARG* 1.3 76.6 - - - +
104A LYS* 1.3 63.9 + - - +
106A ALA* 3.5 5.9 + - - +
107A ALA* 3.2 21.1 + - - +
110A ARG* 4.7 2.1 + - - -
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Residues in contact with LYS 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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26A SER* 4.2 14.1 - - - +
92A GLN* 3.9 15.3 - - - +
100A GLN* 3.1 30.6 + - + +
101A GLN* 4.1 2.9 - - - +
103A SER* 1.3 76.6 - - - +
105A SER* 1.3 59.0 + - - +
107A ALA* 3.4 1.3 + - - -
108A LEU* 3.0 29.1 + - - +
413A MSE 4.0 27.1 - - + +
415A ASP* 4.4 11.7 + - - +
417A PHE 4.2 10.3 + - - -
420A THR 2.8 29.2 + - - +
421A GLY 4.3 0.4 - - - -
422A HIS 2.9 28.9 + - - +
423A LEU* 3.5 27.5 - - + +
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Residues in contact with SER 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 GLN 2.8 23.4 + - - -
102A ARG* 3.9 5.4 - - - -
104A LYS* 1.3 76.2 - - - +
106A ALA* 1.3 58.7 + - - +
108A LEU* 3.3 1.4 + - - -
109A ALA* 2.9 30.9 + - - +
116A VAL* 3.5 24.1 - - - +
119A VAL* 3.6 23.4 - - - +
413A MSE 3.7 13.4 - - - +
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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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102A ARG* 3.0 19.6 + - + +
103A SER* 3.8 6.7 - - - +
104A LYS 3.2 0.4 - - - -
105A SER* 1.3 76.6 - - - +
107A ALA* 1.3 61.5 + - - +
109A ALA* 3.4 6.4 + - - +
110A ARG* 3.1 48.5 + - + +
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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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26A SER* 4.6 9.4 - - - +
103A SER 3.2 11.5 + - - +
104A LYS* 3.7 8.3 - - - +
105A SER 3.3 0.2 - - - -
106A ALA* 1.3 76.9 - - - +
108A LEU* 1.3 63.1 + - - +
110A ARG* 3.4 22.2 + - - +
111A LEU* 3.1 30.4 + - + +
391A PRO* 6.5 0.4 - - + -
423A LEU* 4.3 12.3 - - + -
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Residues in contact with LEU 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 LYS 3.0 17.2 + - - +
105A SER 3.3 3.6 + - - +
107A ALA* 1.3 76.1 - - - +
109A ALA* 1.3 56.8 + - - +
111A LEU* 3.2 7.3 + - + +
112A MSE 3.0 48.5 + - + +
116A VAL* 3.9 17.0 - - + -
391A PRO* 4.3 19.3 - - + -
394A LEU* 4.3 3.1 - - + -
411A LEU* 4.0 15.5 - - + -
412A ALA 3.8 11.7 - - - +
413A MSE 4.0 15.9 - - + -
423A LEU* 4.5 8.5 - - + +
425A SER* 3.7 37.9 - - - +
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Residues in contact with ALA 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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105A SER 2.9 16.6 + - - +
106A ALA* 3.8 7.4 - - - +
108A LEU* 1.3 75.9 - - - +
110A ARG* 1.3 57.4 + - + +
112A MSE 4.9 0.2 - - - -
113A LYS* 2.9 26.2 + - - -
114A HIS 3.1 31.5 + - - +
115A ASP* 4.5 2.2 - - - -
116A VAL* 4.1 13.0 - - + +
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Residues in contact with ARG 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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23A ASP* 5.3 10.5 + - - -
103A SER 4.7 2.0 + - - -
106A ALA* 3.1 32.0 + - + +
107A ALA* 3.5 30.2 - - - +
108A LEU 3.3 0.2 - - - -
109A ALA* 1.3 76.0 - - + +
111A LEU* 1.3 66.6 + - + +
112A MSE 3.6 0.2 + - - -
113A LYS* 3.7 16.9 + - - +
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Residues in contact with LEU 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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107A ALA* 3.1 18.7 + - + +
108A LEU* 3.2 8.3 + - - +
110A ARG* 1.3 81.5 - - + +
112A MSE 1.3 63.7 + - + +
113A LYS* 3.6 9.7 + - - +
391A PRO* 3.7 43.7 - - + +
392A ALA* 4.2 7.6 - - + +
395A ALA* 4.0 20.5 - - + +
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Residues in contact with MSE 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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108A LEU* 3.0 30.5 + - + +
109A ALA 4.3 0.2 - - - +
111A LEU* 1.3 76.6 - - + +
113A LYS* 1.3 70.0 + - - +
114A HIS* 3.3 9.1 + - + +
391A PRO 5.0 1.3 - - - +
394A LEU* 3.8 21.5 - - - -
395A ALA* 3.9 20.0 - - - -
398A SER* 3.1 29.8 - - - +
402A LEU* 5.9 1.6 - - - +
408A ILE* 3.8 30.7 - - + +
411A LEU* 3.9 27.1 - - + -
427A VAL* 4.1 22.2 - - + -
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Residues in contact with LYS 113 (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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109A ALA 2.9 9.1 + - - -
110A ARG* 3.7 12.6 + - - +
111A LEU 3.3 10.3 + - - +
112A MSE 1.3 80.7 - - - +
114A HIS* 1.3 61.9 + - - +
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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