Contacts of the strand formed by residues 103 - 117 (chain A) in PDB entry 4R7X
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 HIS 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 3.3 4.0 - - - -
44A VAL* 2.6 46.9 + - + +
89A ILE* 4.0 26.1 - - + +
102A PHE* 1.3 75.0 - - - +
104A THR* 1.3 87.4 + - - +
105A ILE* 3.6 14.7 - - + +
112A TYR* 5.0 0.7 - + - -
206A PO4 3.4 26.9 + - - -
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Residues in contact with THR 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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41A GLU* 3.3 37.7 - - + +
42A ILE 3.6 5.4 - - - +
43A ARG* 4.0 18.6 + - + +
102A PHE 5.2 1.4 + - - -
103A HIS* 1.3 93.2 + - - +
105A ILE* 1.3 63.9 + - - +
106A HIS* 4.0 18.8 - - + +
206A PO4 5.7 0.5 + - - -
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Residues in contact with ILE 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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36A LEU* 4.2 12.8 - - + -
38A VAL* 3.9 13.1 - - + +
41A GLU* 3.3 3.8 - - - +
42A ILE* 2.9 42.1 + - + +
44A VAL* 3.9 25.6 - - + -
89A ILE* 4.5 6.1 - - + -
103A HIS* 3.6 16.6 - - + +
104A THR* 1.3 82.7 - - - +
106A HIS* 1.3 69.2 + - - +
110A HIS* 3.3 33.7 - - + +
112A TYR* 3.2 26.5 - - + +
206A PO4 4.4 2.5 - - - +
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Residues in contact with HIS 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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38A VAL* 3.3 10.6 - - - +
40A GLY 3.3 8.9 + - - +
41A GLU* 4.0 30.7 - - - +
104A THR* 4.0 15.2 - - + +
105A ILE* 1.3 81.0 - - - +
107A SER* 1.3 64.3 + - - +
110A HIS* 2.8 28.4 + - + +
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Residues in contact with SER 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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38A VAL 3.3 12.1 - - - -
39A THR* 3.9 1.5 - - - -
40A GLY* 2.7 34.2 + - - -
106A HIS* 1.3 83.6 - - - +
108A GLY* 1.3 59.7 + - - +
110A HIS* 3.9 4.3 + - - -
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Residues in contact with GLY 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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36A LEU 3.8 0.2 - - - +
37A GLU* 4.7 4.7 - - - -
38A VAL* 3.2 25.6 + - - +
107A SER* 1.3 76.9 - - - +
109A ARG* 1.3 62.5 + - - -
110A HIS* 3.2 16.8 - - - -
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Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 5.4 0.6 + - - -
33A ARG* 4.5 6.7 - - - +
35A ASN* 3.9 29.1 + - - +
36A LEU 3.8 5.2 - - - +
37A GLU* 4.4 25.7 + - + +
108A GLY* 1.3 74.0 - - - -
110A HIS* 1.3 67.8 + - - +
111A GLU* 3.1 38.5 + - + +
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Residues in contact with HIS 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 VAL 3.6 1.2 - - - +
35A ASN* 3.5 4.0 - - - +
36A LEU* 2.9 43.2 + - + +
38A VAL* 3.9 3.1 - - + -
105A ILE* 3.3 27.0 - - + +
106A HIS* 2.8 29.9 + - + -
107A SER 3.9 5.4 + - - -
108A GLY 3.2 25.7 + - - -
109A ARG* 1.3 77.5 + - - +
111A GLU* 1.3 65.9 + - - +
112A TYR* 3.5 18.2 + - + +
206A PO4 2.4 40.1 + - - +
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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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33A ARG* 3.4 38.6 + - + -
34A VAL 3.7 3.4 - - - -
35A ASN* 3.8 13.5 - - - +
109A ARG* 3.1 25.6 + - + +
110A HIS* 1.3 79.8 - - - +
112A TYR* 1.3 74.6 + - - +
113A ALA 4.2 1.0 + - - -
206A PO4 4.8 3.1 + - - -
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Residues in contact with TYR 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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33A ARG* 4.1 1.3 - - - -
34A VAL* 2.8 47.2 + - + +
36A LEU* 4.3 13.9 - - + -
47A LEU* 3.7 26.2 - - + -
88A LEU* 3.9 16.8 - - + +
89A ILE* 3.6 28.3 - - + -
103A HIS* 5.8 0.2 - + - -
105A ILE* 3.2 19.8 - - - +
110A HIS* 3.5 21.6 - - + +
111A GLU* 1.3 80.3 - - - +
113A ALA* 1.3 65.2 + - - +
114A PHE 3.6 0.5 + - - -
206A PO4 2.9 42.9 + - - -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 3.3 10.1 - - - +
33A ARG* 4.1 7.8 - - + +
88A LEU* 3.4 18.0 - - - +
111A GLU 4.2 1.2 + - - -
112A TYR* 1.3 71.9 - - - +
114A PHE* 1.3 60.2 + - - +
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.9 23.1 - - + -
12A SER 4.1 2.0 - - - -
13A PHE* 4.2 13.5 - + - -
30A VAL* 4.4 0.4 - - + -
31A SER* 3.3 11.3 - - - -
32A GLY* 2.7 72.8 + - - +
33A ARG 3.5 14.4 - - - -
34A VAL* 3.7 22.0 - - + -
49A ILE* 3.7 31.0 - - + -
86A ASP* 6.0 0.9 - - - +
88A LEU* 4.1 13.5 - - + -
113A ALA* 1.3 76.3 - - - +
115A SER* 1.3 66.8 + - - +
116A PHE* 4.3 20.2 - + - -
138A VAL* 4.3 10.8 - - + -
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Residues in contact with SER 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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29A THR* 3.3 24.9 - - - +
30A VAL 3.6 6.5 - - - -
31A SER* 3.8 7.4 - - - -
49A ILE* 5.1 2.4 - - - +
84A HIS* 5.1 1.7 + - - -
86A ASP* 4.9 9.5 + - - +
114A PHE* 1.3 78.2 - - - +
116A PHE* 1.3 62.5 + - - +
117A GLU* 5.9 0.2 - - - +
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Residues in contact with PHE 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 THR* 3.4 7.7 - - - +
30A VAL* 3.0 63.5 + - + +
49A ILE* 4.5 11.2 - - + -
51A ALA* 3.6 22.7 - - + -
82A PHE* 3.8 34.8 - + - -
84A HIS* 3.5 30.5 - + + +
114A PHE* 4.3 14.8 - + - -
115A SER* 1.3 76.1 - - - +
117A GLU* 1.3 72.6 + - - +
118A LEU* 3.9 8.7 - - + -
138A VAL* 3.9 20.2 - - + -
156A PHE* 4.5 3.6 - + - -
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Residues in contact with GLU 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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27A GLY* 4.8 6.2 - - - +
28A ASP 3.6 9.9 - - - +
29A THR* 3.9 18.0 + - + +
82A PHE* 4.0 13.0 - - - -
84A HIS* 5.6 3.2 + - - -
115A SER* 5.9 0.2 - - - +
116A PHE* 1.3 89.4 - - - +
118A LEU* 1.3 68.5 + - - +
119A PRO* 3.9 1.0 - - - +
120A GLN* 5.9 1.0 + - - -
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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