Contacts of the strand formed by residues 41 - 49 (chain A) in PDB entry 3ATI
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 HIS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER* 2.7 25.5 + - - +
36A LEU 3.5 5.6 - - - -
37A ASN* 3.6 6.6 - - - +
40A TYR* 1.3 80.9 - - - +
42A PHE* 1.3 60.3 + - - +
43A CYS 3.1 30.9 + - - -
44A GLY* 4.0 1.1 - - - -
73A ILE* 3.5 25.1 - - + +
139A TRP* 3.7 41.4 - + + +
149A TYR* 6.2 2.2 - + - -
193A GLY* 3.0 28.9 + - - -
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Residues in contact with PHE 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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36A LEU* 3.0 48.2 + - + -
37A ASN 3.9 1.8 - - - -
38A SER* 3.5 28.5 - - - -
40A TYR* 3.8 16.6 - - + -
41A HIS* 1.3 78.6 - - - +
43A CYS* 1.3 88.6 + - + +
59A CYS* 3.2 26.0 - - + -
61A LYS* 3.7 38.1 - - + +
64A ILE* 3.9 13.2 - - + -
193A GLY* 4.5 10.5 - - - -
195A SER* 5.0 0.5 - - - -
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Residues in contact with CYS 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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36A LEU* 2.9 30.4 + - + -
41A HIS* 3.1 17.7 + - - -
42A PHE* 1.3 104.8 - - + +
44A GLY* 1.3 63.4 + - - +
58A HIS* 4.9 2.0 - - - -
59A CYS* 2.0 54.5 - - + -
193A GLY 4.2 2.7 - - - -
195A SER* 3.4 15.0 - - - -
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Residues in contact with GLY 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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33A GLN* 3.8 11.2 - - - -
34A VAL 3.4 11.4 - - - -
36A LEU* 3.9 4.9 - - - +
41A HIS* 4.0 4.8 - - - -
43A CYS* 1.3 78.0 - - - +
45A GLY* 1.3 52.5 + - - -
55A SER* 2.8 27.5 + - - -
193A GLY 4.2 4.0 + - - -
194A ASP 4.4 1.3 + - - -
195A SER 2.8 10.7 + - - -
196A GLY* 3.2 11.5 - - - +
197A GLY* 4.1 4.9 - - - -
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Residues in contact with GLY 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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33A GLN* 3.7 8.1 + - - -
34A VAL* 3.0 42.3 + - - +
36A LEU* 5.1 0.7 - - - -
44A GLY* 1.3 74.1 - - - -
46A SER* 1.3 62.8 + - - -
53A VAL* 4.0 5.2 - - - -
54A VAL 3.3 13.0 - - - -
55A SER* 4.2 1.3 - - - -
196A GLY 3.4 5.8 + - - -
197A GLY* 4.0 1.4 - - - -
198A PRO* 4.0 3.3 - - - +
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Residues in contact with SER 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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32A TYR* 3.3 6.5 - - - -
45A GLY* 1.3 74.6 - - - -
47A LEU* 1.3 62.5 + - - +
48A ILE* 3.4 2.6 + - - +
53A VAL* 3.3 5.4 - - - +
54A VAL 2.9 34.0 + - - -
121A ILE* 4.0 13.0 - - - -
196A GLY 4.9 0.2 + - - -
197A GLY 4.3 0.9 - - - -
198A PRO* 3.2 32.0 - - - +
205A LEU* 3.5 28.1 - - - +
208A ILE* 6.0 0.7 - - - +
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Residues in contact with LEU 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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31A PRO 5.1 0.7 - - - +
32A TYR* 2.8 18.4 + - - +
34A VAL* 4.1 9.0 - - + +
46A SER* 1.3 70.7 - - - +
48A ILE* 1.3 58.2 + - - +
49A ASN 3.0 24.2 - - - +
50A SER 4.6 1.6 - - - +
52A TRP 3.5 10.8 - - - +
53A VAL* 4.0 14.6 - - + -
68A LEU* 4.4 17.7 - - + -
108A LEU* 4.5 9.9 - - + -
112A ALA* 4.7 0.7 - - + -
114A LEU* 3.7 30.3 - - + -
118A VAL* 4.0 16.4 - - + -
119A ALA 4.0 18.6 - - - +
120A SER* 3.2 2.3 - - - +
121A ILE* 2.8 28.4 + - - +
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Residues in contact with ILE 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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46A SER 3.4 5.8 + - - +
47A LEU* 1.3 76.9 - - - +
49A ASN* 1.3 66.5 + - - +
52A TRP* 3.0 27.4 + - + +
54A VAL* 3.4 35.2 - - + -
105A LEU* 4.0 8.5 - - + -
120A SER* 3.6 10.3 - - - -
121A ILE* 3.8 27.9 - - + +
122A SER* 5.8 0.2 - - - -
123A LEU* 4.2 21.4 - - + +
205A LEU* 4.3 5.8 - - + -
234A ILE* 3.8 24.0 - - + -
238A ILE* 4.8 4.9 - - + -
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Residues in contact with ASN 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 LEU* 3.0 24.9 - - - +
48A ILE* 1.3 80.7 + - - +
50A SER* 1.3 65.1 + - - +
51A GLN* 2.9 17.3 + - - +
52A TRP* 3.0 35.7 + - - +
114A LEU* 5.0 0.9 - - - -
120A SER* 3.9 11.4 - - - -
238A ILE* 4.0 17.0 - - - +
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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