Contacts of the strand formed by residues 24 - 33 (chain I) in PDB entry 3A13
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 ASP 24 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17I TYR* 2.5 30.7 + - - -
19I PRO* 3.4 13.0 - - + +
20I SER* 2.8 32.3 + - - +
22I LYS 3.8 0.2 - - - -
23I ARG* 1.3 82.0 - - - +
25I ILE* 1.3 65.6 + - - +
26I ILE* 4.6 1.1 - - + -
90I ALA* 4.3 11.4 - - + -
91I TYR 3.4 2.8 - - - +
92I PRO* 3.5 23.7 - - - +
127I TYR* 3.4 18.7 - - - -
129I PRO* 3.4 16.9 - - - +
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Residues in contact with ILE 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ARG 4.1 0.4 + - - -
24I ASP* 1.3 73.5 - - - +
26I ILE* 1.3 66.4 + - - +
90I ALA* 3.4 3.6 - - - -
91I TYR* 2.7 48.9 + - + +
93I PHE* 4.3 10.3 - - - +
96I PHE* 3.4 34.5 - - + -
104I LEU* 4.5 11.0 - - + -
108I ILE* 5.7 0.9 - - + -
126I LEU* 4.1 21.5 - - + -
127I TYR 3.4 12.3 - - - +
128I PHE* 4.4 4.7 - - + -
129I PRO* 3.8 11.7 - - + -
132I LEU* 3.4 34.3 - - + -
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Residues in contact with ILE 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PRO* 3.8 24.7 - - + -
20I SER 5.6 0.9 - - - +
21I LYS* 6.5 0.4 - - - -
24I ASP* 4.0 4.0 + - + +
25I ILE* 1.3 84.3 - - - +
27I ALA* 1.3 70.8 + - - +
28I VAL* 4.0 1.2 + - - +
75I TYR* 3.4 35.0 - - + +
88I ARG* 4.0 6.1 - - + -
89I ILE 3.3 11.0 - - - +
90I ALA* 4.5 2.7 - - + -
125I ASP 3.8 1.0 - - - +
126I LEU* 3.4 4.9 - - - +
127I TYR* 2.8 52.5 + - + -
352I LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ILE* 1.3 74.5 - - - +
28I VAL* 1.3 60.7 + - - +
29I PHE* 3.5 28.0 - - + -
87I VAL 3.6 1.7 - - - +
88I ARG* 3.5 2.1 - - - -
89I ILE* 2.9 32.7 + - + +
91I TYR* 3.9 18.1 - - + -
108I ILE* 4.3 4.5 - - + -
123I LEU* 3.9 11.9 - - + -
125I ASP 3.6 4.5 - - - -
126I LEU* 4.1 11.4 - - + -
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Residues in contact with VAL 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ILE* 4.5 0.9 - - + +
27I ALA* 1.3 76.1 - - - +
29I PHE* 1.3 58.2 + - - +
86I ILE* 3.5 27.6 - - + -
87I VAL 3.6 4.0 - - - +
88I ARG* 4.2 13.5 - - + +
123I LEU* 3.6 4.3 - - - +
124I GLU* 2.6 39.1 + - + -
125I ASP* 2.9 29.2 + - + +
349I VAL 4.5 0.7 - - - +
350I PHE 3.4 20.0 - - - +
352I LEU* 3.8 33.9 - - + -
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Residues in contact with PHE 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA* 3.5 30.3 - - + -
28I VAL* 1.3 74.4 - - - +
30I ARG* 1.3 58.6 + - - +
31I VAL* 3.6 9.0 + - + -
46I VAL* 3.9 12.8 - - + -
85I TRP 3.4 0.7 - - - +
86I ILE* 3.3 5.9 - - - +
87I VAL* 2.7 38.8 + - + +
89I ILE* 3.8 25.1 - - + -
91I TYR* 4.0 6.7 - - - -
108I ILE 3.5 20.2 - - - -
112I ILE* 3.5 26.0 - - + -
113I PHE* 5.3 1.6 - + - -
121I LEU* 3.6 32.1 - - + -
122I ARG 3.2 4.0 - - - -
123I LEU* 3.7 28.7 - - + -
124I GLU* 4.5 2.7 - - - -
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Residues in contact with ARG 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE* 1.3 69.3 - - - +
31I VAL* 1.3 61.4 + - - +
32I THR* 4.0 0.8 + - - +
80I MET* 3.7 22.6 - - - +
82I ASP* 2.5 31.3 + - - -
84I SER* 2.8 26.2 + - - +
85I TRP 3.2 3.8 - - - +
86I ILE* 3.7 16.8 - - + -
120I GLY 3.9 1.2 - - - +
121I LEU* 3.5 4.0 + - - -
122I ARG* 2.7 37.5 + - + +
124I GLU* 3.7 20.2 + - - +
292I PRO* 3.5 30.2 + - - +
293I TYR* 3.5 23.0 + - + +
350I PHE* 3.8 22.2 - - - -
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Residues in contact with VAL 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE* 3.8 19.5 - - + -
30I ARG* 1.3 75.2 - - - +
32I THR* 1.3 67.6 + - - +
33I PRO* 3.6 5.2 - - - +
39I ILE* 3.8 15.3 - - + +
42I ALA* 3.8 32.1 - - + +
43I ALA* 5.2 5.4 - - - -
46I VAL* 5.2 3.1 - - + -
84I SER* 3.3 2.1 - - - -
85I TRP 2.7 33.9 + - - +
87I VAL* 3.6 25.6 - - + -
89I ILE* 6.3 0.7 - - + -
118I VAL* 4.2 13.5 - - + -
120I GLY 3.7 3.1 - - - +
121I LEU* 3.8 9.6 - - + -
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Residues in contact with THR 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ARG* 4.0 1.2 + - - +
31I VAL* 1.3 74.3 - - - +
33I PRO* 1.3 57.5 - - - +
82I ASP 5.9 0.2 - - - +
83I GLY* 3.7 18.2 - - - +
84I SER* 3.3 17.7 - - - -
118I VAL* 3.5 3.1 - - - -
119I LYS* 2.6 58.0 + - + +
120I GLY* 2.8 26.8 + - - -
293I TYR* 4.2 15.6 + - - +
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Residues in contact with PRO 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I VAL* 3.6 8.7 - - - +
32I THR* 1.3 87.3 - - - +
34I ALA* 1.3 65.1 + - - +
37I TYR 3.5 23.3 - - - +
38I THR 4.1 0.7 - - - +
39I ILE* 3.8 35.4 - - + +
42I ALA* 4.1 14.4 - - + -
83I GLY 3.4 17.7 - - - +
85I TRP* 4.6 4.0 - - + +
117I ARG 3.7 8.1 - - - +
119I LYS* 4.0 11.6 + - - +
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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