Contacts of the strand formed by residues 154 - 163 (chain J) 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 GLY 154 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25I SER 3.3 9.2 - - - -
26I GLU* 3.7 11.7 + - - -
33I ALA* 4.4 3.4 - - - -
81J ILE* 3.3 6.6 - - - +
82J SER 2.9 34.0 + - - -
89J ILE* 3.6 6.5 - - - +
148J HIS* 3.9 9.0 - - - -
150J VAL* 3.9 3.9 - - - +
153J LEU* 1.3 75.0 - - - +
155J CYS* 1.3 60.1 + - - -
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Residues in contact with CYS 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I SER* 3.0 28.0 - - - -
25I SER 2.9 10.3 + - - -
33I ALA* 3.7 21.8 - - + +
34I PHE* 3.8 23.8 - - - -
37I ALA* 3.8 17.2 - - - +
79J TYR* 4.5 2.7 - - - -
80J ILE 3.2 11.2 - - - +
81J ILE* 3.9 16.4 - - + -
89J ILE* 4.1 2.6 - - - +
148J HIS* 4.3 2.7 - - - -
154J GLY* 1.3 75.9 - - - +
156J ALA* 1.3 72.8 + - - +
157J PHE* 4.4 1.6 - - - -
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Residues in contact with ALA 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLY 3.8 4.0 - - - -
24I SER* 4.2 3.1 - - - -
79J TYR* 3.1 7.4 - - - +
80J ILE* 3.0 45.2 + - + +
89J ILE* 3.8 26.8 - - + +
90J SER* 3.9 12.6 - - - -
91J ALA* 3.7 3.9 - - - +
146J VAL* 4.4 7.2 - - + +
148J HIS* 4.5 5.4 - - + -
155J CYS* 1.3 73.9 - - - +
157J PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 4.7 1.3 - - + -
22I ALA* 3.2 2.8 - - - -
23I GLY 2.8 41.7 + - - +
34I PHE* 3.9 14.1 - + - -
37I ALA* 3.8 15.9 - - + -
38I LEU* 3.7 34.5 - - + -
41I ALA* 4.2 17.5 - - + -
43I ILE* 4.3 13.0 - - + -
48I LEU* 3.9 13.2 - - + -
77J TYR* 3.5 29.6 - + + -
78J GLY 3.5 13.2 - - - -
79J TYR* 4.0 4.7 - - + -
91J ALA* 3.8 3.3 - - - +
146J VAL* 3.3 5.0 - - - +
155J CYS* 4.4 1.3 - - - -
156J ALA* 1.3 76.6 - - - +
158J ALA* 1.3 60.4 + - - +
159J ALA* 3.5 28.7 - - + -
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Residues in contact with ALA 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL 3.4 9.0 - - - +
22I ALA* 4.1 7.2 - - + +
77J TYR* 3.3 3.9 - - - +
78J GLY 2.9 32.2 + - - +
91J ALA* 3.7 29.1 - - + +
92J ALA* 3.7 6.7 - - - +
93J ILE* 3.3 18.6 - - + +
144J ILE* 4.6 3.1 - - + +
157J PHE* 1.3 76.7 - - - +
159J ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I LEU* 3.3 6.6 - - - +
21I VAL* 2.8 45.6 + - + +
43I ILE* 5.9 0.7 - - + -
75J THR* 3.6 12.6 - - + -
76J ALA 3.2 12.1 - - - +
77J TYR* 3.5 11.7 - - + -
93J ILE* 3.4 8.5 - - - +
157J PHE* 3.5 19.9 - - + -
158J ALA* 1.3 77.1 - - - +
160J ALA* 1.3 60.7 + - - +
161J ALA 4.0 0.9 - - - -
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Residues in contact with ALA 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I VAL* 4.0 13.7 - - + -
19I SER 3.3 6.3 - - - -
20I LEU* 3.7 19.3 - - + -
51I ILE* 4.9 0.2 - - - +
75J THR* 3.5 3.4 - - - +
76J ALA* 2.8 31.9 + - - +
93J ILE* 3.8 2.7 - - + +
107J ILE* 3.7 32.9 - - + +
159J ALA* 1.3 72.5 - - - +
161J ALA* 1.3 61.5 + - - +
162J LEU* 3.9 4.2 + - - +
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Residues in contact with ALA 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I THR* 5.2 0.2 + - - -
18I VAL* 3.3 4.1 - - - -
19I SER* 2.8 41.7 + - - +
21I VAL* 5.5 2.9 - - + -
43I ILE* 4.0 19.7 - - + -
64J LEU* 4.4 15.5 - - + -
67J LEU* 5.6 0.4 - - + -
73J VAL* 3.9 19.1 - - + -
74J PRO 3.9 4.3 - - - -
75J THR* 4.1 5.2 - - + +
159J ALA 4.0 0.6 - - - -
160J ALA* 1.3 71.8 - - - +
162J LEU* 1.3 62.7 + - - +
163J TRP* 3.9 2.9 + - + +
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Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ASN* 3.9 11.0 - - - +
72H LEU* 4.6 1.1 - - + -
15I PRO* 3.7 26.0 - - + -
17I THR 3.3 12.6 - - - +
18I VAL* 3.8 22.7 - - + -
51I ILE* 3.8 26.5 - - + -
54J ILE 3.8 15.0 - - - +
55J MET* 4.7 1.1 - - + -
56J PRO* 4.3 17.7 - - + -
73J VAL* 3.6 4.2 - - - +
74J PRO* 2.9 42.7 + - + +
107J ILE* 4.4 10.1 - - + -
160J ALA 4.9 2.2 - - - +
161J ALA* 1.3 70.8 - - - +
163J TRP* 1.3 67.7 + - - +
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Residues in contact with TRP 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I GLU* 6.1 2.0 - - - -
5I ILE* 4.1 30.7 - - + -
7I PRO* 5.3 0.7 - - + -
15I PRO* 3.3 3.9 - - - +
16I ASN 3.0 24.3 + - - -
17I THR* 3.0 24.1 + - - +
19I SER* 6.0 0.7 - - - +
65J PRO* 4.2 23.3 - - + +
66J LYS 4.8 5.3 + - - -
67J LEU* 3.7 30.4 - - + +
68J PRO* 4.3 15.9 - - + +
71J ALA* 4.1 16.2 - - + -
72J LEU 3.7 21.1 - - - -
73J VAL* 4.2 14.1 - - + -
74J PRO* 4.5 2.2 - - + -
161J ALA* 3.9 3.7 + - + +
162J LEU* 1.3 83.3 - - - +
164J TYR* 1.3 104.9 + + + +
14K LEU* 5.9 0.9 - - + -
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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