Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 5T5W
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 LYS 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN 3.3 5.4 - - - +
31A SER* 3.2 17.7 - - - -
32A VAL* 3.0 17.9 + - + +
33A ASN* 3.1 3.4 + - + +
34A PHE* 1.3 74.3 - - - +
36A ASN* 1.3 59.9 + - - +
37A ILE* 3.6 28.0 + - + +
75A ASP* 5.6 2.2 - - - +
77A SER* 3.5 12.8 - - - +
137A GLU* 4.5 29.2 - - + +
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Residues in contact with ASN 36 (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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29A MET* 3.5 20.0 - - - -
30A ASN 3.9 0.9 - - - -
31A SER* 2.4 25.6 + - - -
34A PHE* 3.3 20.5 + - - +
35A LYS* 1.3 69.6 - - - +
37A ILE* 1.3 59.0 + - - +
75A ASP* 3.6 3.3 - - - +
76A PHE* 2.7 59.9 + - + +
77A SER* 3.2 16.8 + - - +
79A LEU* 4.4 7.7 + - - +
81A LYS* 5.8 1.4 - - - +
105A PHE* 3.5 22.0 - - + -
107A PRO* 4.8 5.7 - - - +
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Residues in contact with ILE 37 (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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29A MET* 3.5 2.8 - - - -
30A ASN* 2.8 45.8 + - + +
35A LYS* 4.1 37.2 - - + +
36A ASN* 1.3 79.0 - - - +
38A LEU* 1.3 60.2 + - - +
39A GLN* 3.3 31.4 + - + +
73A GLU* 3.9 24.7 - - + +
74A CYS 3.5 4.3 - - - +
75A ASP* 3.9 26.9 - - + +
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Residues in contact with LEU 38 (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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27A VAL* 4.1 11.4 - - + -
28A ARG 3.3 17.9 - - - +
29A MET* 3.7 11.3 - - + +
36A ASN 4.0 0.2 + - - -
37A ILE* 1.3 68.9 - - - +
39A GLN* 1.3 58.8 + - - +
40A TRP* 3.2 26.0 - - + -
54A ALA* 4.1 10.8 - - + -
73A GLU* 3.1 5.2 - - - -
74A CYS 2.9 29.8 + - - +
76A PHE* 3.6 36.6 - - + -
87A LEU* 4.6 10.8 - - + -
88A ARG 5.0 2.5 - - - +
89A VAL* 4.3 13.2 - - + -
103A ILE* 3.7 26.9 - - + -
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Residues in contact with GLN 39 (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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27A VAL* 3.7 1.4 - - - +
28A ARG* 3.0 69.5 + - + +
30A ASN* 3.7 31.7 + - + +
37A ILE* 3.3 24.7 + - + +
38A LEU* 1.3 76.4 - - - +
40A TRP* 1.3 65.3 + - - +
72A THR* 3.7 4.7 - - - +
73A GLU* 4.1 19.7 + - + +
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Residues in contact with TRP 40 (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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24A PRO* 4.0 13.7 - - + -
25A GLU 3.9 8.3 - - - +
26A ASN 3.8 7.9 - - - -
27A VAL* 4.1 15.9 - - + -
28A ARG* 4.4 7.0 + - - +
38A LEU* 3.2 51.1 - - + -
39A GLN* 1.3 78.7 - - - +
41A GLU* 1.3 71.3 + - - +
52A PHE* 3.4 47.7 - + + -
54A ALA* 4.8 3.1 - - + -
66A CYS* 5.6 2.0 - - + -
69A THR* 4.9 3.8 - - - -
71A LEU 3.4 18.4 - - - -
72A THR* 3.1 38.3 + - - +
73A GLU* 3.6 21.5 - - - -
74A CYS* 3.7 9.0 - - + -
89A VAL* 4.2 15.7 - - + -
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Residues in contact with GLU 41 (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 GLU* 3.1 40.8 + - + +
26A ASN* 4.4 9.8 + - + +
28A ARG* 4.8 4.2 - - - +
40A TRP* 1.3 80.0 - - - +
42A SER* 1.3 67.8 + - - +
43A PRO* 3.5 1.9 - - - +
72A THR* 5.2 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