Contacts of the helix formed by residues 105 - 118 (chain A) in PDB entry 1SQV
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 ASP 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A MET* 3.7 39.9 - - - +
101A ALA* 4.5 4.0 - - + -
102A LEU* 3.0 36.1 + - + +
104A LYS* 1.3 105.8 + - - +
106A LEU* 1.3 56.8 + - - +
107A PRO* 3.4 4.5 - - - -
108A LYS* 3.4 6.4 + - + +
109A ALA* 2.8 30.3 + - - +
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Residues in contact with LEU 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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35A CYS* 4.2 11.2 - - - -
37A VAL* 3.5 39.7 - - + -
102A LEU 3.8 1.7 + - - -
103A SER 3.1 14.2 + - - +
105A ASP* 1.3 75.1 - - - +
107A PRO* 1.3 73.7 - - + +
109A ALA* 3.5 6.0 - - - +
110A VAL* 3.0 24.8 + - + +
199A ALA* 4.6 1.1 - - + -
203A LEU* 3.9 29.2 - - + -
207A GLN* 3.4 31.6 - - + +
208A LEU* 4.2 13.0 - - + +
211A LEU* 4.3 13.2 - - + -
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Residues in contact with PRO 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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103A SER 4.6 0.9 - - - +
104A LYS 3.8 19.7 - - - +
105A ASP* 4.1 0.7 - - - -
106A LEU* 1.3 93.6 - - + +
108A LYS* 1.3 60.1 + - + +
110A VAL* 3.0 3.5 + - - +
111A GLU* 2.9 26.7 + - - +
207A GLN* 5.6 2.7 - - - +
211A LEU* 3.7 30.1 - - + +
215A HIS* 5.6 0.2 - - - -
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Residues in contact with LYS 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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70A ARG* 4.4 1.6 - - - +
78A GLU* 3.4 29.4 - - + +
82A MET* 4.8 15.3 - - + -
105A ASP* 3.4 6.9 + - + +
107A PRO* 1.3 77.2 - - + +
109A ALA* 1.3 58.8 + - - +
111A GLU* 3.2 40.7 + - + +
112A LEU* 2.9 43.9 + - + +
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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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37A VAL* 3.8 19.7 - - + -
82A MET* 4.6 5.7 - - + +
99A ILE* 3.4 25.3 - - + +
101A ALA* 4.8 12.6 - - + -
105A ASP 2.8 20.8 + - - +
106A LEU* 3.5 12.3 - - - +
108A LYS* 1.3 77.4 - - - +
110A VAL* 1.3 62.8 + - - +
113A LEU* 3.1 22.7 + - - +
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Residues in contact with VAL 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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37A VAL* 3.9 26.7 - - + -
106A LEU* 3.0 22.8 + - + +
107A PRO 3.6 2.9 - - - +
109A ALA* 1.3 72.1 - - - +
111A GLU* 1.3 67.1 + - - +
113A LEU* 2.8 20.9 + - - +
114A ALA* 3.0 11.4 + - - +
197A LEU* 4.5 6.5 - - + -
208A LEU* 4.1 16.6 - - + -
211A LEU* 3.7 34.8 - - + +
215A HIS* 4.4 3.1 - - + -
216A PHE* 3.6 24.9 - - + -
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Residues in contact with GLU 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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70A ARG* 2.7 33.6 + - - +
107A PRO 2.9 13.7 + - - +
108A LYS* 3.2 38.7 + - + +
110A VAL* 1.3 74.2 - - - +
112A LEU* 1.3 60.8 + - - +
114A ALA* 3.4 3.8 - - - +
115A ASP* 3.2 22.2 + - - +
215A HIS* 3.6 38.4 + - + +
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Residues in contact with LEU 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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70A ARG* 3.6 44.4 - - - +
75A LEU* 3.8 17.0 - - + +
78A GLU* 4.2 19.3 - - + +
79A VAL* 3.5 31.2 - - + -
82A MET* 4.5 13.0 - - + -
99A ILE* 4.3 7.9 - - + -
108A LYS* 2.9 29.5 + - + +
109A ALA 3.6 3.8 - - - +
111A GLU* 1.3 73.2 - - - +
113A LEU* 1.3 61.3 + - - +
115A ASP* 3.0 8.0 + - + +
116A ILE* 2.9 32.5 + - + +
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Residues in contact with LEU 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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37A VAL* 3.8 34.3 - - + +
38A GLY* 3.7 13.9 - - - -
39A VAL* 4.3 7.3 - - + +
86A LEU* 5.2 3.1 - - + -
97A TYR* 3.6 37.5 - - + +
98A TYR 4.5 0.2 - - - -
99A ILE* 3.7 22.7 - - + -
109A ALA 3.1 22.7 + - - +
110A VAL* 2.8 11.9 + - - +
112A LEU* 1.3 72.2 - - - +
114A ALA* 1.3 56.3 + - - +
116A ILE* 3.4 11.6 + - + +
117A VAL* 3.0 32.7 + - - +
197A LEU* 4.6 5.4 - - + -
216A PHE* 4.1 9.9 - - + -
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Residues in contact with ALA 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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110A VAL 3.0 7.2 + - - +
111A GLU 3.4 10.5 - - - +
113A LEU* 1.3 74.5 - - - +
115A ASP* 1.3 62.9 + - - +
117A VAL* 3.2 2.6 + - - +
118A GLN* 2.7 35.6 + - - +
215A HIS* 3.3 42.4 - - + +
216A PHE* 3.6 19.9 - - + -
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Residues in contact with ASP 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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67A THR* 2.6 32.8 + - + +
69A ASN* 3.0 28.1 - - - +
70A ARG* 3.1 31.7 + - - +
75A LEU* 6.0 1.1 - - + +
111A GLU 3.2 10.0 + - - +
112A LEU* 3.0 11.2 + - + +
114A ALA* 1.3 77.4 - - - +
116A ILE* 1.3 57.9 + - + +
118A GLN* 4.7 0.2 - - - +
119A ASN* 2.9 45.3 + - - +
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Residues in contact with ILE 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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63A ALA* 3.5 27.9 - - + +
64A PHE* 4.4 11.4 - - + -
67A THR* 4.3 8.7 - - + -
75A LEU* 3.8 41.5 - - + -
86A LEU* 4.2 21.8 - - + -
97A TYR* 4.7 15.0 - - + -
112A LEU* 2.9 28.0 + - + +
113A LEU* 3.6 12.8 - - + +
115A ASP* 1.3 79.5 - - + +
117A VAL* 1.3 62.8 + - + +
118A GLN 3.3 0.7 + - - -
120A CYS* 3.8 22.3 + - - +
186A LEU* 6.0 0.2 - - - +
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Residues in contact with VAL 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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39A VAL* 4.0 11.0 - - + -
41A ILE* 3.9 24.2 - - + -
97A TYR* 4.6 7.2 - - + -
113A LEU 3.0 19.2 + - - +
114A ALA 3.2 6.7 + - - +
116A ILE* 1.3 77.6 - - + +
118A GLN* 1.3 67.3 + - + +
186A LEU* 5.0 3.4 - - - +
190A TYR* 3.7 34.2 - - + +
195A MET* 3.7 26.3 - - + +
216A PHE* 3.6 24.7 - - + -
219A LEU* 5.4 1.6 - - - +
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Residues in contact with GLN 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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114A ALA* 2.7 33.5 + - - +
117A VAL* 1.3 87.8 - - + +
119A ASN* 1.3 76.8 + - - +
120A CYS* 2.9 14.0 + - - +
186A LEU* 4.4 10.4 - - - +
215A HIS 3.4 21.3 + - - +
216A PHE* 4.1 10.9 - - - -
217A SER 4.1 10.6 - - - +
218A GLY 4.5 2.8 - - - +
219A LEU* 4.1 33.9 - - + +
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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