Contacts of the strand formed by residues 88 - 98 (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 THR 88 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86H GLY 3.6 5.6 + - - -
87H GLU* 1.3 75.5 - - - +
89H ILE* 1.3 64.1 + - - +
113H LYS* 3.5 22.9 - - - +
114H CYS* 3.6 23.4 + - - +
115H SER* 4.5 2.5 - - - -
147H GLU* 4.3 26.0 - - + +
148H HIS 3.4 8.5 - - - +
149H THR* 3.6 17.2 + - - +
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Residues in contact with ILE 89 (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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80H ILE* 3.5 50.9 - - + +
82H SER* 3.9 22.4 - - - +
87H GLU* 4.2 10.3 - - + +
88H THR* 1.3 79.9 - - - +
90H SER* 1.3 63.5 + - - +
112H GLY 3.5 3.6 - - - -
113H LYS* 4.2 3.8 - - + -
114H CYS 3.9 0.4 - - - -
147H GLU* 3.2 2.3 - - - +
148H HIS* 2.8 44.7 + - + +
150H VAL* 4.1 12.8 - - + -
154H GLY 3.6 24.5 - - - +
155H CYS 4.3 0.2 - - - -
156H ALA* 3.8 12.8 - - + +
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Residues in contact with SER 90 (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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80H ILE* 3.4 5.4 - - - +
89H ILE* 1.3 71.4 - - - +
91H ALA* 1.3 61.0 + - - +
111H GLU* 3.2 3.7 - - - -
112H GLY 2.9 33.2 + - - -
114H CYS* 2.8 23.0 + - - -
115H SER 3.2 7.1 - - - -
116H LYS* 4.2 0.9 - - - -
119H ALA* 3.7 24.0 - - - -
146H VAL 3.1 10.3 - - - -
147H GLU* 3.1 23.0 - - - +
156H ALA* 3.9 4.5 - - - -
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Residues in contact with ALA 91 (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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78H GLY 3.8 9.2 - - - +
90H SER* 1.3 76.9 - - - +
92H ALA* 1.3 61.5 + - - +
110H TYR 3.3 9.0 - - - +
111H GLU* 4.6 2.2 - - + -
119H ALA* 4.6 1.6 - - - -
145H ALA* 3.3 2.7 - - - +
146H VAL* 3.0 31.3 + - + +
156H ALA* 3.7 23.0 - - - +
157H PHE* 3.7 6.3 - - - +
158H ALA* 3.6 24.0 - - - +
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Residues in contact with ALA 92 (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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78H GLY 5.5 0.2 + - - -
91H ALA* 1.3 76.7 - - - +
93H ILE* 1.3 61.5 + - - +
109H GLU* 3.4 4.7 - - - +
110H TYR* 2.8 32.2 + - + +
119H ALA* 3.6 20.2 - - + +
120H GLU 4.0 0.4 - - - +
123H VAL* 3.6 22.2 - - + -
144H ILE 3.3 13.7 - - - +
145H ALA* 3.6 12.3 - - + -
158H ALA* 3.5 7.4 - - - +
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Residues in contact with ILE 93 (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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20G LEU* 3.9 11.4 - - + -
76H ALA 3.8 21.5 - - - +
92H ALA* 1.3 74.2 - - - +
94H SER* 1.3 62.2 + - - +
107H ILE* 3.8 17.7 - - + -
108H MET 3.4 15.0 - - - +
109H GLU* 3.9 16.6 - - + +
123H VAL* 4.0 2.4 - - - +
143H SER* 3.2 5.9 - - - -
144H ILE* 3.0 53.2 + - + +
158H ALA* 4.1 8.1 - - + +
159H ALA* 3.7 27.8 - - - +
160H ALA* 3.9 10.8 - - + +
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Residues in contact with SER 94 (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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20G LEU* 5.0 0.2 - - - -
93H ILE* 1.3 76.2 - - - +
95H VAL* 1.3 68.2 + - - +
106H LEU 3.8 0.6 - - - +
107H ILE* 3.3 6.1 - - - +
108H MET* 2.9 34.4 + - - +
123H VAL* 2.8 41.6 + - - +
124H ARG* 4.2 0.4 - - - -
127H ALA* 3.4 10.0 - - - +
141H ILE* 4.1 11.4 - - - -
142H GLU 3.2 6.5 - - - -
143H SER* 3.8 9.6 - - - -
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Residues in contact with VAL 95 (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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18G VAL* 4.5 4.3 - - + -
20G LEU* 3.6 30.3 - - + -
55H MET* 4.0 29.4 - - + -
61H ILE* 4.1 14.1 - - + -
94H SER* 1.3 81.1 - - - +
96H ALA* 1.3 69.7 + - - +
97H ILE* 3.7 6.9 + - + +
106H LEU 3.3 7.6 - - - +
107H ILE* 4.1 20.9 - - + -
140H ARG 3.8 0.3 - - - +
141H ILE* 3.2 5.6 - - - -
142H GLU* 2.8 38.2 + - + +
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Residues in contact with ALA 96 (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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95H VAL* 1.3 72.3 - - - +
97H ILE* 1.3 59.3 - - - +
105H GLY* 3.1 7.8 - - - -
106H LEU* 2.8 35.2 + - + +
127H ALA* 4.0 22.7 - - + +
131H PHE* 3.5 27.7 - - + -
138H LEU* 3.8 15.3 - - + -
140H ARG 3.6 4.9 - - - -
141H ILE* 4.1 5.6 - - + -
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Residues in contact with ILE 97 (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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55H MET* 4.1 20.6 - - + -
61H ILE* 4.0 20.0 - - + -
95H VAL* 4.2 9.9 - - + +
96H ALA* 1.3 77.1 - - - +
98H PRO* 1.3 76.7 - - + +
101H LYS* 3.9 15.3 - - + +
105H GLY* 4.7 0.4 - - - -
131H PHE* 3.9 1.8 - - - -
138H LEU* 3.7 3.3 - - - +
139H ASP* 2.8 31.0 + - + +
140H ARG* 2.8 60.5 + - + +
142H GLU* 4.0 8.1 - - + +
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Residues in contact with PRO 98 (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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55H MET* 5.0 2.9 - - + -
96H ALA 3.9 0.7 - - - +
97H ILE* 1.3 90.0 - - + +
99H LYS* 1.3 65.5 + - - +
100H ASP 3.5 21.5 - - - +
101H LYS* 3.1 26.0 + - + +
103H LEU* 3.6 25.4 - - + +
104H CYS 3.5 24.5 - - - +
105H GLY* 3.9 8.3 - - - -
131H PHE* 3.6 21.3 - - + -
136H TRP* 4.8 0.2 - - + -
137H GLU 3.6 2.0 - - - +
139H ASP* 3.6 1.2 - - - +
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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