Contacts of the strand formed by residues 114 - 125 (chain N) in PDB entry 5HJD
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 VAL 114 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15N HIS* 3.3 33.0 - - + +
16N ARG* 3.2 6.4 - - - +
17N ALA* 3.0 44.3 + - + +
105N PHE* 3.7 24.9 - - + +
106N LEU* 3.8 1.1 - - - -
107N HIS* 3.1 51.6 + - + +
113N PRO* 1.3 74.5 - - - +
115N ASN* 1.3 64.2 + - - +
116N HIS* 4.4 4.0 - - + +
201N SO4 5.2 1.3 - - - +
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Residues in contact with ASN 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N HIS 3.8 2.8 - - - +
16N ARG* 3.2 30.4 + - - +
35N PHE* 6.2 0.3 - - - -
107N HIS* 5.1 0.4 - - - -
113N PRO 3.4 5.8 + - - +
114N VAL* 1.3 76.1 - - - +
116N HIS* 1.3 61.6 + - - +
117N LEU 4.3 0.3 + - - -
201N SO4 3.2 8.2 + - - -
16Q ARG* 2.5 44.6 + - - +
113Q PRO* 5.9 4.4 - - - +
114Q VAL 5.1 2.0 + - - -
115Q ASN* 3.2 41.2 + - - +
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Residues in contact with HIS 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N GLY* 3.4 2.9 - - - -
15N HIS* 3.0 49.7 + + + +
35N PHE* 5.2 0.5 - - - -
102N TYR* 3.6 26.5 - + - -
103N ASP 5.5 0.9 - - - -
105N PHE* 5.3 6.4 - + + -
114N VAL* 4.6 3.8 - - + -
115N ASN* 1.3 76.1 - - - +
117N LEU* 1.3 91.7 + - - +
118N ARG* 4.4 7.1 - - + +
201N SO4 3.0 34.8 + - - +
37Q ARG* 4.3 12.7 + - - -
40Q GLU* 5.6 14.8 - - + +
115Q ASN* 4.7 0.7 + - - -
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Residues in contact with LEU 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N GLU* 3.5 23.8 - - + +
13N LEU 3.8 4.9 - - - +
14N GLY* 4.0 4.7 - - - -
35N PHE* 3.7 28.9 - - + -
37N ARG* 4.5 3.4 - - - +
115N ASN 4.3 0.4 + - - -
116N HIS* 1.3 88.2 + - - +
118N ARG* 1.3 59.7 + - - +
12Q GLU* 4.9 0.7 - - - +
37Q ARG* 3.1 27.5 + - - +
115Q ASN* 3.2 50.0 - - + +
116Q HIS 4.3 0.4 - - - -
117Q LEU* 3.4 34.1 - - + +
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Residues in contact with ARG 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N GLU* 3.4 3.7 - - - -
13N LEU* 2.7 55.0 + - + +
100N PHE* 3.7 29.7 - - - +
101N ASP 3.2 29.7 + - - +
102N TYR* 4.0 20.4 - - + +
103N ASP 4.8 1.2 - - - +
116N HIS* 4.4 12.8 - - + +
117N LEU* 1.3 77.2 - - - +
119N CYS* 1.3 61.7 + - - +
120N GLU* 2.9 36.3 + - + +
12Q GLU* 5.0 2.7 - - - +
40Q GLU* 5.2 21.2 + - + +
117Q LEU* 4.2 2.5 - - - -
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Residues in contact with CYS 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU 3.7 5.8 - - - +
12N GLU* 4.4 5.8 - - + +
39N PRO* 6.4 1.3 - - + -
118N ARG* 1.3 74.1 - - - +
120N GLU* 1.3 72.0 + - - +
12Q GLU* 3.3 16.6 + - - +
117Q LEU* 4.0 8.4 - - + +
119Q CYS* 2.0 46.7 - - + -
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Residues in contact with GLU 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N LYS* 3.9 2.8 - - - +
11N LEU* 2.8 43.8 + - + +
13N LEU* 4.4 13.2 - - + -
100N PHE* 3.6 42.0 - - + -
118N ARG* 2.9 41.2 + - + +
119N CYS* 1.3 80.8 - - - +
121N LYS* 1.3 63.6 + - - +
122N LEU* 4.3 1.5 + - + +
40Q GLU* 5.2 3.8 - - - +
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Residues in contact with LYS 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N GLN* 3.2 41.0 + - + +
9N VAL 3.9 9.6 - - - +
10N LYS* 4.8 14.6 - - + +
100N PHE* 5.5 0.5 - - - -
120N GLU* 1.3 82.2 + - - +
122N LEU* 1.3 76.1 + - - +
123N THR* 4.2 5.3 + - + +
202N SO4 2.8 51.2 + - - +
10Q LYS* 6.2 1.6 - - - +
121Q LYS* 5.0 4.9 - - - +
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Residues in contact with LEU 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N VAL 3.4 1.2 - - - +
8N GLN* 3.3 6.1 - - - +
9N VAL* 3.0 53.8 + - + +
11N LEU* 3.7 31.9 - - + -
47N PHE* 4.6 0.7 - - + -
89N PHE* 3.7 30.3 - - + -
98N VAL* 3.8 29.6 - - + -
100N PHE* 3.9 13.7 - - + -
120N GLU 5.2 0.9 - - - +
121N LYS* 1.3 84.1 - - - +
123N THR* 1.3 59.9 + - - +
124N PHE* 4.1 8.7 - - + -
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Residues in contact with THR 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ALA* 4.1 17.3 - - - +
7N VAL 3.0 9.9 + - - -
8N GLN* 4.5 12.0 + - - +
121N LYS* 5.3 4.9 - - + +
122N LEU* 1.3 73.4 - - - +
124N PHE* 1.3 63.9 + - - +
125N ASN* 3.9 19.3 + - - +
202N SO4 5.5 7.2 - - - +
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Residues in contact with PHE 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N CYS 3.4 1.0 - - - +
6N ALA* 3.4 2.4 - - - -
7N VAL* 2.8 58.7 + - + +
9N VAL* 3.9 19.1 - - + -
89N PHE* 3.6 46.7 - + - -
95N PRO* 4.8 22.4 - - + -
122N LEU* 4.1 11.0 - - + -
123N THR* 1.3 75.3 - - - +
125N ASN* 1.3 62.4 + - - +
126N ASN 3.9 0.2 - - - -
127N PRO* 4.5 8.7 - - + -
131N PHE* 3.9 23.6 - + - -
135N LEU* 3.7 31.9 - - + -
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Residues in contact with ASN 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N CYS 3.7 3.4 - - - +
6N ALA* 4.3 10.9 - - - +
123N THR* 3.9 22.8 + - - +
124N PHE* 1.3 71.0 - - - +
126N ASN* 1.3 79.0 + - + +
127N PRO* 3.6 1.1 - - - +
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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