Contacts of the strand formed by residues 138 - 149 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ALA* 3.6 24.2 - - + -
97B ILE 3.6 9.6 - - - +
99B LYS* 3.9 12.3 + - - -
128B LYS* 4.6 19.5 - - + -
131B PHE* 3.8 20.9 - - + -
136B TRP 3.3 4.1 + - - +
137B GLU* 1.3 72.5 - - - +
139B ASP* 1.3 58.3 + - - +
140B ARG* 3.5 24.7 - - - +
141B ILE* 3.8 24.2 - - + -
63H PRO* 3.3 47.8 - - + +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 2.8 20.2 + - + +
98B PRO 3.6 17.9 - - - +
99B LYS* 3.8 15.5 - - - +
101B LYS* 4.5 8.0 + - - -
137B GLU 3.8 1.6 + - - -
138B LEU* 1.3 74.7 - - - +
140B ARG* 1.3 96.8 + - - +
20G LEU 3.9 18.1 - - - +
21G VAL* 4.3 12.9 - - - +
22G ALA 4.9 3.6 + - - +
41G ALA 4.2 2.8 - - - +
63H PRO* 3.8 0.5 - - - +
64H LEU* 2.9 26.3 + - - +
144H ILE* 5.1 2.4 - - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 5.7 2.2 - - - +
97B ILE* 2.9 59.1 + - + +
101B LYS* 4.6 5.1 - - - +
138B LEU* 3.5 9.3 - - - +
139B ASP* 1.3 120.1 + - - +
141B ILE* 1.3 67.0 - - - +
142B GLU* 2.9 27.5 + - - +
22G ALA 5.3 1.2 + - - -
39G LEU 4.4 3.0 + - - -
40G ASN* 3.2 22.8 + - - +
41G ALA* 3.2 18.2 + - - +
42G GLY* 3.4 18.9 - - - +
63H PRO* 5.0 0.4 - - - -
64H LEU* 3.7 31.9 - - + +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B SER* 3.9 18.6 - - - -
95B VAL 3.3 9.4 - - - +
96B ALA* 4.1 4.9 - - - -
124B ARG* 2.8 72.1 + - + +
127B ALA* 4.3 1.6 - - + -
128B LYS* 4.0 17.3 - - + +
138B LEU* 3.8 28.7 - - + -
140B ARG* 1.3 83.6 - - - +
142B GLU* 1.3 76.7 + - - +
64H LEU 4.7 2.2 + - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.1 10.0 - - + +
61B ILE* 3.7 35.0 - - + -
94B SER* 3.2 2.8 - - - -
95B VAL* 2.7 34.0 + - + +
97B ILE* 3.9 13.2 - - + -
124B ARG* 4.2 0.2 - - - +
140B ARG* 2.9 28.7 + - - +
141B ILE* 1.3 79.3 - - - +
143B SER* 1.3 62.2 + - - +
39G LEU 5.4 0.7 - - - +
42G GLY* 4.2 8.7 - - - +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.9 9.1 - - - +
93B ILE 3.1 16.4 - - - -
94B SER* 3.9 2.9 - - - -
120B GLU* 2.7 30.5 + - - +
123B VAL* 4.7 0.7 - - - -
124B ARG* 2.9 38.5 + - - +
142B GLU* 1.3 77.3 + - - +
144B ILE* 1.3 63.1 + - - +
66H LYS* 5.1 0.2 - - - -
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.8 33.4 - - + +
21A VAL* 3.8 34.1 - - - +
22A ALA* 3.8 14.8 - - + +
92B ALA* 3.3 3.1 - - - +
93B ILE* 2.9 46.3 + - + +
120B GLU* 4.3 5.3 - - - +
143B SER* 1.3 77.3 - - - +
145B ALA* 1.3 69.1 + - - +
158B ALA* 4.6 1.6 - - + -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 4.5 4.2 - - - +
91B ALA 3.4 6.7 - - - +
92B ALA* 3.8 10.3 - - + -
116B LYS* 3.2 44.4 + - + +
119B ALA* 5.0 0.7 - - + -
120B GLU* 3.7 29.0 - - + +
144B ILE* 1.3 83.4 - - - +
146B VAL* 1.3 63.7 + - - +
158B ALA* 5.2 0.2 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 3.8 10.1 - - + -
23A GLY* 3.7 26.9 - - - +
24A SER* 4.4 6.5 - - - +
40A ASN* 5.7 0.2 - - - +
90B SER* 3.1 6.4 - - - -
91B ALA* 3.0 38.8 + - + +
116B LYS* 4.3 6.5 - - - -
145B ALA* 1.3 76.8 - - - +
147B GLU* 1.3 71.4 + - - +
156B ALA* 4.4 3.3 - - + +
157B PHE 3.3 34.8 - - - +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 4.2 4.2 + - - -
88B THR* 3.9 17.6 + - + +
89B ILE 3.2 5.6 - - - +
90B SER* 3.0 17.9 - - - +
115B SER* 3.5 10.7 - - - -
116B LYS* 2.9 40.3 + - + +
146B VAL* 1.3 84.0 - - - +
148B HIS* 1.3 61.9 + - - +
149B THR* 4.6 7.1 + - - -
156B ALA* 5.0 0.9 - - - -
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Residues in contact with HIS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 3.1 31.2 + - - -
25A SER* 4.0 19.1 - - - -
26A GLU* 2.8 33.4 + - + -
87B GLU 3.5 0.9 - - - +
88B THR* 3.4 3.4 - - - -
89B ILE* 2.7 52.1 + - + +
147B GLU* 1.3 76.8 - - - +
149B THR* 1.3 77.3 + - - +
150B VAL* 3.8 6.7 - - + -
151B GLU* 5.5 2.7 - - - -
154B GLY* 3.7 18.7 - - - -
155B CYS 4.2 5.8 - - - +
156B ALA* 4.4 1.8 - - + -
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU* 4.1 0.2 - - - +
86B GLY* 3.8 25.6 - - - +
87B GLU 3.5 3.1 - - - -
88B THR* 3.8 16.2 + - - +
147B GLU* 4.6 6.4 + - - -
148B HIS* 1.3 85.3 + - - +
150B VAL* 1.3 66.9 + - - +
151B GLU* 3.5 9.2 + - - +
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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