Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 4XXL
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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102A ALA* 1.3 76.7 - - - +
104A PRO* 1.3 74.3 - - - +
105A GLU* 3.6 10.5 + - - +
106A ALA* 2.9 26.8 + - - +
107A ILE* 3.1 21.6 + - - +
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Residues in contact with PRO 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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76A ILE* 5.9 0.3 - - - +
102A ALA 4.0 4.0 - - - +
103A SER* 1.3 87.4 - - - +
105A GLU* 1.3 62.2 + - - +
107A ILE* 3.3 10.0 + - + +
108A LYS* 3.0 25.5 + - - +
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Residues in contact with GLU 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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30A ASP* 6.1 0.5 - - - +
103A SER* 3.2 8.8 + - - +
104A PRO* 1.3 78.0 - - - +
106A ALA* 1.3 69.8 + - - +
108A LYS* 3.4 8.0 + - + +
109A ASN* 3.0 36.7 + - - +
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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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33A ALA* 6.6 0.2 - - + -
34A ALA* 5.8 0.5 - - - -
37A LEU* 3.6 26.5 - - + +
102A ALA* 4.5 3.1 - - + -
103A SER* 2.9 26.1 + - - +
105A GLU* 1.3 85.3 + - - +
107A ILE* 1.3 65.4 + - - +
109A ASN* 3.3 6.7 + - - +
110A LEU 3.0 19.2 + - - -
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Residues in contact with ILE 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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37A LEU* 4.2 5.2 - - + -
76A ILE* 4.5 16.6 - - + -
79A VAL* 3.9 26.2 - - + -
80A THR* 4.2 16.4 - - + -
98A ILE* 3.8 41.3 - - + +
99A ASN* 5.0 3.4 - - - +
100A GLY 5.3 0.9 - - - +
102A ALA* 3.9 19.5 - - + +
103A SER 3.1 20.6 + - - +
104A PRO* 3.8 7.0 - - + +
106A ALA* 1.3 77.7 - - - +
108A LYS* 1.3 65.3 + - - +
110A LEU* 3.2 5.0 + - + +
111A VAL* 3.0 23.7 + - + +
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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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72A GLU* 3.0 34.5 + - - +
76A ILE* 4.2 18.6 - - + +
104A PRO 3.0 17.7 + - - +
105A GLU* 3.7 6.7 - - - +
107A ILE* 1.3 78.2 - - - +
109A ASN* 1.3 57.4 + - - +
111A VAL* 3.4 2.1 + - - +
112A ASP* 2.9 57.6 + - - +
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Residues in contact with ASN 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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28A ALA 4.5 1.6 - - - +
29A VAL* 3.5 10.8 - - - +
30A ASP* 2.9 50.4 + - - +
33A ALA* 4.0 9.5 - - - +
34A ALA* 3.5 15.8 - - - +
105A GLU* 3.0 30.8 + - - +
106A ALA* 3.3 7.4 + - - +
108A LYS* 1.3 76.4 - - - +
110A LEU* 1.3 57.7 + - - +
112A ASP* 3.3 8.0 + - - +
113A TRP* 3.0 28.1 + - - +
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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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34A ALA* 3.7 28.3 - - + +
37A LEU* 4.0 25.4 - - + -
38A ALA* 4.3 14.6 - - + +
43A CYS* 4.7 4.9 - - - -
58A TYR* 5.7 0.7 - - + -
79A VAL* 5.7 1.1 - - + -
98A ILE* 4.7 10.8 - - + -
106A ALA 3.0 13.5 + - - +
107A ILE* 3.2 7.6 + - + +
109A ASN* 1.3 77.9 - - - +
111A VAL* 1.3 64.6 + - + +
113A TRP* 3.2 21.5 + - + +
114A ILE* 3.0 34.2 + - + +
201A HEC 3.9 22.2 - - + -
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Residues in contact with VAL 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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72A GLU* 3.7 22.4 - - + +
75A LEU* 3.6 31.4 - - + +
76A ILE* 3.9 26.5 - - + +
79A VAL* 4.7 9.6 - - + -
107A ILE 3.0 19.5 + - - +
108A LYS 3.7 4.0 - - - +
110A LEU* 1.3 78.0 - - + +
112A ASP* 1.3 64.4 + - - +
114A ILE* 3.2 11.1 + - + +
115A LEU* 2.9 37.8 + - + +
201A HEC 6.5 0.4 - - + -
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Residues in contact with ASP 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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29A VAL* 3.8 21.7 - - + +
72A GLU* 2.5 31.1 - - - +
108A LYS* 2.9 46.0 + - - +
109A ASN* 3.8 6.1 - - - +
110A LEU 3.2 0.4 - - - -
111A VAL* 1.3 76.1 - - - +
113A TRP* 1.3 63.7 + - - +
115A LEU* 3.4 8.8 + - - +
116A SER* 3.2 20.4 + - - -
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Residues in contact with TRP 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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29A VAL* 3.7 12.7 - - + +
31A VAL* 3.9 33.3 - - + +
34A ALA* 3.6 18.2 - - + -
35A LYS* 3.9 28.3 - - + -
38A ALA* 5.1 0.2 - - + -
44A PHE* 3.9 27.1 - + - -
49A VAL* 3.7 26.5 - - + -
58A TYR* 4.3 9.6 - + - -
109A ASN 3.0 13.6 + - - +
110A LEU* 3.2 27.1 + - + +
112A ASP* 1.3 76.0 - - - +
114A ILE* 1.3 74.0 + - + +
116A SER* 2.6 31.5 + - - -
117A LEU* 3.5 34.0 - - + +
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Residues in contact with ILE 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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58A TYR* 3.9 51.5 - - + +
61A VAL* 4.0 26.9 - - + -
62A ALA* 3.3 9.1 - - - +
75A LEU* 4.1 10.5 - - + -
110A LEU* 3.0 26.2 + - + +
111A VAL* 3.2 12.5 + - + +
113A TRP* 1.3 85.0 - - + +
115A LEU* 1.3 63.8 + - - +
117A LEU* 3.1 23.8 + - - +
201A HEC 4.0 26.2 - - + -
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Residues in contact with LEU 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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61A VAL* 5.3 0.2 - - + -
62A ALA* 3.6 14.0 - - - +
65A TYR* 3.6 32.8 - - + -
66A ARG* 6.0 0.3 - - - -
71A ALA* 3.9 10.1 - - + +
72A GLU* 3.7 36.3 - - + +
75A LEU* 3.6 20.2 - - + -
111A VAL* 2.9 27.2 + - + +
112A ASP* 3.4 8.9 + - - +
114A ILE* 1.3 75.0 - - + +
116A SER* 1.3 60.1 + - - +
117A LEU 3.3 0.2 - - - -
118A TRP* 3.5 19.6 + - - -
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Residues in contact with SER 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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29A VAL* 5.4 5.6 - - - +
112A ASP 3.2 10.8 + - - -
113A TRP* 2.6 31.3 + - - -
115A LEU* 1.3 77.4 - - - +
117A LEU* 1.3 59.9 + - - +
118A TRP* 3.2 15.5 + - - +
119A SER* 3.6 17.0 + - - -
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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