Contacts of the strand formed by residues 72 - 82 (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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.5 34.1 - - + +
49A ILE* 4.0 16.4 - - + +
70B GLY 4.0 3.8 - - - +
71B ALA* 1.3 69.5 - - - +
73B VAL* 1.3 60.4 + - - +
74B PRO* 3.4 11.8 - - - +
163B TRP* 3.5 12.7 - - - -
7E PRO* 3.5 44.1 - - + +
8E LEU* 5.5 5.9 - - + +
11E TYR* 5.3 5.1 + - - +
13E LYS 5.8 0.9 - - - +
14E LEU* 5.2 2.1 - - + +
15E PRO* 4.4 17.0 - - + -
51E ILE* 4.3 6.1 - - + -
74F PRO* 3.6 28.9 - - + -
162F LEU* 4.5 5.2 - - + -
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Residues in contact with VAL 73 (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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43A ILE* 6.3 0.4 - - + -
46A VAL* 4.0 22.4 - - + -
47A ASN 2.8 13.1 + - - +
48A LEU* 3.6 2.8 - - + -
49A ILE* 2.9 23.3 + - - -
67B LEU* 4.2 17.9 - - + -
71B ALA* 3.7 23.6 - - + +
72B LEU* 1.3 71.9 - - - +
74B PRO* 1.4 61.2 - - - +
75B THR* 2.9 24.3 + - - +
161B ALA* 4.0 15.9 - - + -
162B LEU 3.5 20.9 - - - +
163B TRP* 4.1 12.3 - - + -
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Residues in contact with PRO 74 (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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15A PRO* 4.9 2.7 - - + -
49A ILE* 3.4 16.8 - - + +
51A ILE* 4.0 17.7 - - + -
72B LEU 3.4 10.3 - - - +
73B VAL* 1.4 79.1 - - - +
75B THR* 1.3 60.7 + - - +
162B LEU* 2.9 54.8 + - + +
163B TRP* 4.3 6.5 - - + -
164B TYR* 4.9 4.0 - - + +
49C ILE* 5.1 2.0 - - + -
72D LEU* 3.8 34.5 - - + -
8E LEU* 5.3 6.7 - - + +
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Residues in contact with THR 75 (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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43A ILE* 4.8 1.3 - - + -
48A LEU* 3.5 27.2 - - + +
49A ILE 2.9 10.0 + - - -
50A ARG* 3.2 8.0 - - - +
51A ILE* 2.9 25.3 + - - +
73B VAL* 2.9 22.8 + - - +
74B PRO* 1.3 74.9 + - - +
76B ALA* 1.3 65.8 + - - +
77B TYR* 3.9 14.2 + - + -
159B ALA* 3.6 25.8 - - + -
160B ALA 3.4 15.5 - - - +
161B ALA* 4.1 5.2 - - + +
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Residues in contact with ALA 76 (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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51A ILE* 3.4 29.3 - - + +
53B PYR 3.9 9.9 - - + +
75B THR* 1.3 71.0 - - - +
77B TYR* 1.3 61.8 + - - +
93B ILE* 3.7 4.5 - - + +
107B ILE* 3.8 29.2 - - + -
109B GLU* 4.7 6.7 - - - +
159B ALA* 3.2 3.1 - - - +
160B ALA* 2.8 35.3 + - + +
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Residues in contact with TYR 77 (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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34A PHE* 4.0 12.3 - + - -
48A LEU* 4.0 21.8 - - + -
50A ARG* 2.8 73.5 + - + +
75B THR* 3.9 14.3 + - + -
76B ALA* 1.3 75.4 - - - +
78B GLY* 1.3 59.8 + - - +
79B TYR* 3.8 21.8 - + - -
93B ILE* 4.0 2.9 - - - +
109B GLU* 3.5 18.1 + - - +
157B PHE* 3.6 14.6 - + + -
158B ALA 3.2 14.1 - - - +
159B ALA* 3.5 11.0 - - + -
7006B MRD 3.6 9.4 - - - +
52E SER* 2.8 33.9 + - - -
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Residues in contact with GLY 78 (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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50A ARG* 4.2 4.3 - - - -
77B TYR* 1.3 75.4 - - - +
79B TYR* 1.3 62.7 + - - +
91B ALA* 3.6 8.6 - - - +
92B ALA 5.3 0.9 - - - -
93B ILE* 4.4 0.2 - - - +
109B GLU* 3.9 18.2 - - - +
110B TYR 4.8 7.2 - - - -
111B GLU* 4.5 6.3 - - - -
157B PHE* 3.6 1.9 - - - -
158B ALA 2.9 31.7 + - - +
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Residues in contact with TYR 79 (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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34A PHE* 3.7 16.8 - + + -
50A ARG* 4.0 24.2 + - - +
77B TYR* 3.8 17.9 - + - -
78B GLY* 1.3 76.1 - - - +
80B ILE* 1.3 67.0 + - - +
81B ILE* 3.9 25.4 - - + -
91B ALA* 4.4 0.2 - - - -
111B GLU* 3.3 23.7 - - - +
155B CYS* 4.4 1.1 - - - -
156B ALA 3.1 13.0 - - - +
157B PHE* 4.0 15.0 - - + -
7006B MRD 3.0 46.4 + - + +
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Residues in contact with ILE 80 (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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79B TYR* 1.3 78.2 - - - +
81B ILE* 1.3 73.9 + - - +
82B SER* 5.4 0.7 - - - -
89B ILE* 3.6 32.2 - - + +
90B SER 3.4 24.7 - - - +
111B GLU* 3.6 17.3 - - - +
112B GLY* 3.6 28.9 - - - +
113B LYS* 3.9 16.6 - - + +
155B CYS* 3.2 4.2 - - - -
156B ALA* 3.0 36.4 + - + +
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Residues in contact with ILE 81 (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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30A PRO* 3.4 39.0 - - + +
34A PHE* 4.4 4.5 - - + -
79B TYR* 3.9 16.9 - - + -
80B ILE* 1.3 85.8 - - - +
82B SER* 1.3 67.4 + - - +
113B LYS* 6.1 0.5 - - - -
153B LEU* 3.7 24.7 - - + -
154B GLY 3.3 10.5 - - - +
155B CYS* 3.8 14.6 - - + -
7006B MRD 3.5 25.6 - - + +
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Residues in contact with SER 82 (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* 5.4 0.7 - - - -
81B ILE* 1.3 79.1 - - - +
83B ASP* 1.3 61.5 + - - +
84B VAL* 3.1 15.9 + - - +
87B GLU* 2.7 29.1 + - - -
89B ILE* 3.8 19.5 - - - +
113B LYS* 5.6 2.5 - - - -
150B VAL* 3.6 13.2 - - - +
153B LEU* 3.3 3.4 - - - +
154B GLY 3.0 31.5 + - - -
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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