Contacts of the strand formed by residues 138 - 149 (chain H) in PDB entry 1N13
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 LEU 138 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96H ALA* 3.8 15.5 - - + -
97H ILE 3.7 8.1 - - - +
99H LYS* 4.2 7.3 - - - +
128H LYS* 4.7 19.3 - - + -
131H PHE* 3.8 21.3 - - + -
136H TRP 3.7 1.0 + - - -
137H GLU* 1.3 73.6 - - - +
139H ASP* 1.3 62.7 + - - +
140H ARG* 3.7 27.1 - - - +
141H ILE* 3.8 24.5 - - + -
7007H MRD 4.6 11.8 - - + +
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Residues in contact with ASP 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ILE* 2.8 19.2 + - + +
98H PRO 3.6 13.7 - - - +
99H LYS* 3.8 10.8 - - - +
101H LYS* 3.0 23.2 + - - +
138H LEU* 1.3 76.4 - - - +
140H ARG* 1.3 95.2 + - - +
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Residues in contact with ARG 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ILE* 5.0 4.8 - - - +
95H VAL 3.8 0.2 - - - +
96H ALA* 3.6 1.7 - - - -
97H ILE* 2.8 55.1 + - + +
101H LYS* 4.9 2.4 - - - +
138H LEU* 3.7 6.9 - - - +
139H ASP* 1.3 112.7 + - - +
141H ILE* 1.3 67.3 + - - +
142H GLU* 2.8 34.9 + - + -
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Residues in contact with ILE 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H SER* 4.1 17.3 - - - -
95H VAL 3.2 12.1 - - - +
96H ALA* 4.1 5.4 - - - -
124H ARG* 2.9 70.9 + - + +
127H ALA* 4.3 5.2 - - + -
128H LYS* 4.0 22.0 - - + +
138H LEU* 3.8 29.4 - - + +
140H ARG* 1.3 81.9 - - - +
142H GLU* 1.3 70.3 + - - +
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Residues in contact with GLU 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 4.7 5.9 + - - +
137B GLU* 4.6 11.8 - - - +
20G LEU* 3.7 14.6 - - + +
61H ILE* 3.4 32.7 - - + +
94H SER* 3.2 2.3 - - - -
95H VAL* 2.8 38.4 + - + +
97H ILE* 4.0 5.8 - - + +
124H ARG* 4.2 0.2 - - - +
140H ARG* 2.8 43.5 + - - +
141H ILE* 1.3 77.1 - - - +
143H SER* 1.3 63.3 + - - +
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Residues in contact with SER 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 5.3 1.0 - - - +
20G LEU* 3.9 4.8 - - - +
93H ILE 3.2 16.2 - - - -
94H SER* 3.8 11.4 - - - -
120H GLU* 2.7 31.1 + - - +
123H VAL* 4.5 0.9 - - - -
124H ARG* 2.9 33.5 + - - +
142H GLU* 1.3 77.2 - - - +
144H ILE* 1.3 74.4 + - - +
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Residues in contact with ILE 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 3.6 37.9 - - + +
139B ASP* 5.1 3.4 - - - +
20G LEU* 3.3 15.5 - - + +
21G VAL* 3.3 47.1 - - - +
22G ALA* 3.8 8.5 - - + +
92H ALA* 3.3 3.5 - - - +
93H ILE* 3.0 42.7 + - + +
116H LYS* 5.8 0.4 - - - +
120H GLU* 4.0 7.4 - - - -
143H SER* 1.3 85.7 - - - +
145H ALA* 1.3 63.5 + - - +
158H ALA* 4.7 0.3 - - - +
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Residues in contact with ALA 145 (chain H).
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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101B LYS* 6.1 0.3 - - - +
22G ALA* 4.4 7.3 - - - +
91H ALA 3.3 12.8 - - - +
92H ALA* 3.6 12.8 - - + +
116H LYS* 3.1 55.1 - - + +
119H ALA* 4.7 0.9 - - + -
120H GLU* 3.8 10.0 - - + -
144H ILE* 1.3 77.9 - - - +
146H VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G ALA* 3.9 9.9 - - + -
23G GLY* 3.7 28.7 - - - +
24G SER* 4.2 7.0 - - - +
40G ASN* 5.4 0.7 - - - +
90H SER* 3.1 6.9 - - - -
91H ALA* 3.0 39.0 + - + +
116H LYS* 4.1 8.3 - - - +
145H ALA* 1.3 78.3 - - - +
147H GLU* 1.3 73.2 + - - +
156H ALA* 4.3 3.6 - - + -
157H PHE 3.5 32.5 - - - +
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Residues in contact with GLU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G SER* 4.0 4.9 + - - -
88H THR* 4.3 12.7 - - + +
89H ILE 3.2 6.1 - - - +
90H SER* 3.1 17.0 - - - +
115H SER* 3.6 11.4 - - - -
116H LYS* 2.9 36.0 + - + +
146H VAL* 1.3 85.0 - - - +
148H HIS* 1.3 64.3 + - - +
149H THR* 5.5 3.5 + - - +
156H ALA* 5.0 0.9 - - - -
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Residues in contact with HIS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G SER* 3.4 29.2 + - - -
25G SER* 3.8 21.8 - - - -
26G GLU* 2.8 34.2 + - + +
87H GLU 3.5 1.0 - - - +
88H THR* 3.4 3.4 - - - -
89H ILE* 2.8 47.2 + - + +
147H GLU* 1.3 76.8 - - - +
149H THR* 1.3 77.0 + - - +
150H VAL* 3.8 5.4 - - + -
151H GLU* 5.5 1.6 - - - -
154H GLY* 3.8 17.8 - - - -
155H CYS 4.3 6.1 - - - +
156H ALA* 4.5 1.6 - - + -
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Residues in contact with THR 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H GLY* 3.7 28.9 - - - +
87H GLU 3.4 3.8 - - - +
88H THR* 3.6 15.5 + - - +
147H GLU* 5.5 2.9 + - - +
148H HIS* 1.3 83.2 + - - +
150H VAL* 1.3 65.7 - - - +
151H GLU* 3.4 11.0 + - + +
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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