Contacts of the strand formed by residues 138 - 149 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96L ALA* 3.6 26.0 - - + -
97L ILE 3.7 6.1 - - - +
99L LYS* 4.5 0.9 - - - -
128L LYS* 4.4 20.2 - - + -
131L PHE* 3.8 19.1 - - + -
136L TRP 3.5 3.2 + - - +
137L GLU* 1.3 80.7 - - - +
139L ASP* 1.3 62.8 + - - +
140L ARG* 3.5 27.6 - - - +
141L ILE* 3.7 25.4 - - + -
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Residues in contact with ASP 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L ILE 2.8 18.4 + - - +
98L PRO 3.7 4.5 - - - +
99L LYS* 3.7 27.1 - - - +
101L LYS* 3.9 11.4 + - - -
137L GLU 3.7 2.0 + - - -
138L LEU* 1.3 76.3 - - - +
140L ARG* 1.3 92.8 + - - +
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Residues in contact with ARG 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L ILE* 5.0 4.6 - - - +
97L ILE* 2.8 59.5 + - + +
101L LYS* 4.5 4.4 - - - +
138L LEU* 3.5 8.4 - - - +
139L ASP* 1.3 107.1 + - - +
141L ILE* 1.3 67.2 + - - +
142L GLU* 3.1 33.2 + - + -
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Residues in contact with ILE 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L SER* 4.0 17.7 - - - -
95L VAL 3.3 10.8 - - - +
96L ALA* 4.3 4.0 - - - -
124L ARG* 2.9 71.9 + - + +
127L ALA* 4.2 4.7 - - + -
128L LYS* 4.0 17.0 - - + +
138L LEU* 3.7 31.2 - - + -
140L ARG* 1.3 82.2 - - - +
142L GLU* 1.3 70.3 + - - +
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Residues in contact with GLU 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K LEU* 3.7 11.4 - - + +
61L ILE* 3.5 45.6 - - + +
94L SER* 3.2 2.1 - - - -
95L VAL 2.8 31.6 + - - -
97L ILE* 4.6 2.7 - - + +
140L ARG* 3.1 41.2 + - - +
141L ILE* 1.3 75.2 - - - +
143L SER* 1.3 61.0 + - - +
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Residues in contact with SER 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K LEU* 3.9 5.5 - - - +
93L ILE 3.2 14.4 - - - -
94L SER* 3.9 5.4 - - - -
120L GLU* 2.7 32.7 + - - +
123L VAL* 4.5 1.1 - - - -
124L ARG* 2.8 44.8 + - - +
142L GLU* 1.3 77.3 - - - +
144L ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K LEU* 3.9 23.1 - - + +
21K VAL* 4.0 11.0 - - - +
22K ALA* 3.8 29.2 - - + +
92L ALA* 3.3 3.5 - - - +
93L ILE* 3.0 55.5 + - + +
120L GLU* 3.9 5.4 - - - -
143L SER* 1.3 76.5 - - - +
145L ALA* 1.3 70.2 - - - +
158L ALA* 4.6 0.6 - - + +
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Residues in contact with ALA 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ALA* 4.5 4.5 - - - +
91L ALA 3.3 7.2 - - - +
92L ALA* 3.6 17.7 - - + +
116L LYS* 3.5 41.4 - - + +
119L ALA* 4.9 0.9 - - + -
120L GLU* 3.8 15.9 + - + +
144L ILE* 1.3 84.3 - - - +
146L VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ALA* 3.9 10.5 - - + -
23K GLY* 3.6 27.6 - - - +
24K SER* 4.2 6.5 - - - +
40K ASN* 5.5 0.7 - - - +
90L SER* 3.2 6.1 - - - -
91L ALA 3.0 36.9 + - - +
116L LYS* 3.9 8.1 - - - -
145L ALA* 1.3 76.6 - - - +
147L GLU* 1.3 71.7 + - - +
156L ALA* 4.4 4.5 - - + -
157L PHE 3.3 33.4 - - - +
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Residues in contact with GLU 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K SER* 4.0 4.7 + - - -
88L THR* 4.2 12.9 - - + +
89L ILE 3.3 6.5 - - - +
90L SER* 3.1 15.9 - - - +
115L SER* 3.6 12.1 - - - -
116L LYS* 2.9 40.0 + - + +
146L VAL* 1.3 84.9 - - - +
148L HIS* 1.3 62.1 + - - +
149L THR* 5.4 3.9 + - - +
156L ALA* 5.0 0.7 - - - -
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Residues in contact with HIS 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K SER* 3.1 30.5 + - - -
25K SER* 3.9 21.1 - - - -
26K GLU* 2.8 34.6 + - + +
87L GLU 3.5 1.2 - - - +
88L THR* 3.3 3.0 - - - -
89L ILE* 2.8 47.1 + - + +
147L GLU* 1.3 77.2 - - - +
149L THR* 1.3 78.2 + - - +
150L VAL* 3.8 4.9 - - + -
151L GLU* 5.5 2.2 - - - -
154L GLY* 3.9 18.8 - - - -
155L CYS 4.3 5.2 - - - +
156L ALA* 4.5 1.6 - - + -
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Residues in contact with THR 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L GLY* 3.8 29.2 - - - +
87L GLU 3.6 2.9 - - - -
88L THR* 3.3 18.1 + - - +
147L GLU* 5.4 4.2 + - - +
148L HIS* 1.3 84.2 + - - +
150L VAL* 1.3 64.9 + - - +
151L GLU* 3.5 10.2 + - - +
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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