Contacts of the strand formed by residues 88 - 98 (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 THR 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLY 3.6 5.8 + - - -
87B GLU* 1.3 76.0 - - - +
89B ILE* 1.3 64.7 + - - +
113B LYS* 3.5 8.3 - - - +
114B CYS* 3.4 36.3 + - - +
115B SER* 4.4 2.7 - - - -
147B GLU* 3.9 28.7 + - - +
148B HIS 3.4 9.0 - - - +
149B THR* 3.8 14.4 + - - +
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Residues in contact with ILE 89 (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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80B ILE* 3.6 40.4 - - + +
82B SER* 3.8 24.2 - - - +
87B GLU* 4.1 13.0 - - + +
88B THR* 1.3 78.6 - - - +
90B SER* 1.3 64.7 + - - +
112B GLY 3.5 4.5 - - - +
113B LYS* 4.5 2.2 - - + -
147B GLU* 3.7 0.3 - - - +
148B HIS* 2.7 50.7 + - + +
150B VAL* 4.1 10.5 - - + -
154B GLY 3.5 31.4 - - - +
155B CYS 4.0 0.9 - - - +
156B ALA* 3.8 13.4 - - + +
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Residues in contact with SER 90 (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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80B ILE* 3.4 5.0 - - - +
89B ILE* 1.3 69.8 - - - +
91B ALA* 1.3 60.8 + - - +
111B GLU* 3.3 3.0 - - - -
112B GLY 3.0 33.7 + - - -
114B CYS* 2.7 24.5 + - - -
115B SER 3.1 16.7 - - - -
116B LYS* 4.1 1.1 - - - -
119B ALA* 3.8 14.1 - - - -
146B VAL 3.1 11.2 - - - -
147B GLU* 3.0 22.7 - - - +
156B ALA* 3.9 4.9 - - - -
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Residues in contact with ALA 91 (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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78B GLY 3.6 25.6 - - - +
79B TYR* 4.4 2.0 - - - -
90B SER* 1.3 75.3 - - - +
92B ALA* 1.3 63.1 + - - +
110B TYR 3.2 8.7 - - - +
111B GLU* 4.6 0.7 - - + -
119B ALA* 4.5 2.1 - - - +
145B ALA* 3.4 1.9 - - - +
146B VAL* 3.0 30.0 + - + +
156B ALA* 3.6 22.6 - - + +
157B PHE 3.8 1.8 - - - +
158B ALA* 3.7 14.1 - - - +
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Residues in contact with ALA 92 (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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78B GLY* 5.3 0.5 - - - -
91B ALA* 1.3 76.5 - - - +
93B ILE* 1.3 66.7 + - - +
109B GLU* 3.4 4.3 - - - +
110B TYR* 2.8 36.0 + - + +
119B ALA* 3.7 18.6 - - + +
120B GLU* 3.9 0.4 - - - +
123B VAL* 3.7 21.8 - - + -
144B ILE 3.3 13.5 - - - +
145B ALA* 3.8 12.1 - - + -
158B ALA* 3.6 3.6 - - - +
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Residues in contact with ILE 93 (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 26.2 - - + -
76B ALA 3.7 19.1 - - - +
77B TYR* 4.0 0.4 - - - -
92B ALA* 1.3 74.1 - - - +
94B SER* 1.3 69.6 + - - +
107B ILE* 4.1 5.2 - - + -
108B MET 3.3 6.5 - - - +
109B GLU* 3.5 28.7 - - + -
123B VAL* 3.9 2.9 - - - -
143B SER* 3.1 6.2 - - - -
144B ILE* 2.9 41.8 + - + +
158B ALA* 3.4 35.8 - - - +
159B ALA 3.5 2.9 - - - +
160B ALA* 4.0 10.5 - - + +
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Residues in contact with SER 94 (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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93B ILE* 1.3 74.5 - - - +
95B VAL* 1.3 65.8 + - - +
96B ALA 4.2 0.4 - - - -
106B LEU 4.2 0.4 - - - -
107B ILE* 3.2 5.7 - - - +
108B MET* 2.9 37.0 + - - +
123B VAL* 2.7 38.3 + - - +
124B ARG* 4.0 1.1 - - - -
127B ALA* 3.4 9.2 - - - +
141B ILE* 3.9 16.2 - - - -
142B GLU 3.2 10.3 - - - -
143B SER* 4.0 2.7 - - - -
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Residues in contact with VAL 95 (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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18A VAL* 4.6 6.1 - - + -
20A LEU* 3.8 28.5 - - + -
55B MET* 3.9 37.2 - - + -
61B ILE* 4.2 16.2 - - + -
94B SER* 1.3 80.2 - - - +
96B ALA* 1.3 64.9 + - - +
97B ILE* 3.6 4.8 + - + +
106B LEU 3.3 7.0 - - - +
107B ILE* 4.0 21.8 - - + -
140B ARG 3.9 0.2 - - - +
141B ILE* 3.3 5.1 - - - -
142B GLU 2.7 34.0 + - - +
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Residues in contact with ALA 96 (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 4.2 0.2 - - - -
95B VAL* 1.3 71.7 - - - +
97B ILE* 1.3 59.5 + - - +
105B GLY* 3.1 8.1 - - - -
106B LEU* 2.8 34.8 + - + +
127B ALA* 3.8 25.0 - - + +
131B PHE* 3.6 23.1 - - + -
138B LEU* 3.6 19.3 - - + -
140B ARG 3.7 5.4 - - - -
141B ILE* 4.1 4.7 - - + -
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Residues in contact with ILE 97 (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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55B MET* 4.0 19.5 - - + -
61B ILE* 3.9 12.6 - - + -
95B VAL* 4.0 9.9 - - + +
96B ALA* 1.3 76.1 - - - +
98B PRO* 1.3 63.3 - - + +
101B LYS* 3.6 25.1 - - - +
105B GLY* 4.7 0.4 - - - -
131B PHE* 4.0 1.8 - - - -
138B LEU* 3.6 4.0 - - - +
139B ASP* 2.8 33.6 + - + +
140B ARG* 2.9 59.3 + - + +
142B GLU* 3.9 17.7 - - + -
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Residues in contact with PRO 98 (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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55B MET* 5.0 2.5 - - + -
97B ILE* 1.3 91.3 - - + +
99B LYS* 1.3 64.1 + - - +
100B ASP 3.4 22.0 - - - +
101B LYS* 3.1 28.2 + - + -
103B LEU* 3.6 23.1 - - + +
104B CYS 3.5 22.9 - - - +
105B GLY* 3.9 7.4 - - - +
131B PHE* 3.5 24.2 - - + -
137B GLU 4.3 1.1 - - - +
139B ASP* 3.6 2.7 - - - +
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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