Contacts of the strand formed by residues 41 - 51 (chain A) in PDB entry 2I69
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 ILE 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL 3.7 0.5 - - - +
32A THR* 3.4 2.8 - - - +
33A ILE* 2.8 55.7 + - + +
39A PRO 3.9 2.5 - - - +
40A THR* 1.3 77.9 - - - +
42A ASP* 1.3 63.8 + - - +
43A VAL* 4.5 6.3 - - + -
141A ILE* 4.7 5.8 - - + -
142A PHE 3.1 14.8 - - - +
143A VAL* 3.9 18.4 - - + -
144A HIS* 3.9 1.1 - - - -
186A VAL* 4.2 12.1 - - + -
290A VAL* 4.2 12.6 - - + -
292A MET* 3.6 32.3 - - + -
295A LEU* 3.9 20.4 - - + -
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PHE 4.9 2.0 - - - +
2A ASN* 3.8 9.2 - - - +
3A CYS* 2.9 44.4 + - - +
4A LEU 4.2 2.1 + - - -
30A CYS* 4.6 1.3 - - - -
31A VAL 3.1 3.8 - - - -
32A THR* 3.0 18.2 + - - -
41A ILE* 1.3 75.0 - - - +
43A VAL* 1.3 63.5 + - - +
44A LYS* 4.2 0.4 + - - -
140A ALA 4.0 0.2 - - - +
141A ILE* 3.4 7.6 - - - +
142A PHE* 2.9 38.1 + - + +
144A HIS* 2.6 35.0 + - - -
152A HIS* 5.3 0.2 + - - -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.5 10.5 - - + -
25A LEU* 3.9 20.4 - - + +
30A CYS* 3.6 1.0 - - - -
31A VAL* 2.6 38.6 + - - +
33A ILE* 3.5 27.8 - - + -
41A ILE* 4.5 8.3 - - + -
42A ASP* 1.3 77.3 - - - +
44A LYS* 1.3 65.4 + - - +
139A VAL* 3.8 21.8 - - + -
140A ALA 3.7 2.9 - - - +
141A ILE* 4.2 17.7 - - + -
188A VAL* 5.5 2.9 - - + -
288A CYS* 6.5 0.4 - - - -
290A VAL* 4.7 13.7 - - + -
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PHE* 3.4 20.7 - - - +
2A ASN 3.1 36.1 + - - +
6A MET* 3.4 27.1 - - - +
25A LEU* 4.5 3.8 - - - -
28A ASP* 6.1 0.4 - - - -
29A SER 3.7 15.9 - - - +
30A CYS* 3.8 8.7 - - - -
42A ASP 5.4 0.4 - - - -
43A VAL* 1.3 79.3 - - - +
45A MET* 1.3 67.7 + - - +
46A MET* 3.5 29.0 + - - +
139A VAL* 3.2 10.3 - - - +
140A ALA* 2.8 40.5 + - + +
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.9 29.7 - - + +
26A GLU 3.3 27.1 - - - +
27A GLY* 4.0 4.5 - - - -
28A ASP* 3.9 18.2 + - - +
29A SER 3.3 7.9 + - - +
44A LYS* 1.3 76.7 - - - +
46A MET* 1.3 61.9 + - - +
47A ASN 3.9 13.9 - - - +
48A MET* 3.5 37.7 - - + -
137A TYR* 3.7 18.2 - - + -
138A GLU 3.8 11.7 - - - +
139A VAL* 4.8 2.2 - - + +
286A LEU* 4.0 18.4 - - + -
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Residues in contact with MET 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PHE* 3.7 25.4 - - + +
28A ASP* 6.0 0.8 - - - -
44A LYS* 3.5 28.3 - - + +
45A MET* 1.3 73.4 - - - +
47A ASN* 1.3 63.9 + - - +
138A GLU 2.7 14.8 + - - +
139A VAL 4.2 0.2 - - - -
140A ALA* 3.7 27.8 - - + +
166A ARG* 3.3 50.7 + - - +
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Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET* 3.3 5.9 - - - +
46A MET* 1.3 85.9 - - + +
48A MET* 1.3 74.9 + - - +
49A GLU* 3.0 41.5 + - - +
136A LYS 4.0 0.6 + - - +
137A TYR* 3.5 1.7 - - - -
138A GLU* 2.7 54.7 + - + +
166A ARG* 4.4 3.8 - - - +
280A LYS* 4.0 25.6 + - - +
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Residues in contact with MET 48 (chain A).
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 4.5 0.2 - - - -
27A GLY* 4.0 17.7 - - - +
45A MET* 3.5 39.0 - - + -
47A ASN* 1.3 83.0 + - - +
49A GLU* 1.3 61.7 + - - +
135A ILE* 5.4 1.1 - - + -
136A LYS 3.3 5.4 - - - +
137A TYR* 3.7 23.1 - - + -
280A LYS* 4.2 1.0 - - - +
281A LEU* 3.1 47.1 + - + +
282A THR 4.7 0.2 - - - +
283A SER 3.3 23.8 - - - +
284A GLY* 3.3 28.0 - - - +
285A HIS* 4.0 2.2 - - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.0 34.0 + - - +
48A MET* 1.3 74.7 - - - +
50A ALA* 1.3 62.7 + - - +
51A ALA* 3.9 4.5 + - + +
134A ASN 3.4 1.6 - - - +
135A ILE* 3.4 3.9 - - - +
136A LYS* 2.8 48.2 + - + +
278A THR* 3.7 29.2 + - - +
279A VAL 3.5 12.1 - - - +
280A LYS* 4.9 10.5 + - - +
281A LEU* 4.2 3.6 - - - -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 1.3 73.5 - - - +
51A ALA* 1.3 59.8 + - - +
53A LEU* 3.8 10.8 - - + +
130A ILE* 3.6 30.1 - - + -
134A ASN* 3.2 10.8 - - + +
135A ILE* 4.5 2.0 - - + -
278A THR* 3.5 1.8 - - - -
279A VAL* 3.0 48.7 + - + +
281A LEU* 3.9 10.1 - - + +
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.9 7.0 - - + +
50A ALA* 1.3 75.0 - - - +
52A ASN* 1.3 82.6 + - - +
53A LEU 3.4 2.7 - - - -
134A ASN* 3.0 28.2 + - - +
136A LYS* 6.4 2.0 - - + -
277A ASN 4.0 4.3 - - - -
278A THR* 3.5 24.7 - - + -
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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