Contacts of the strand formed by residues 28 - 38 (chain A) in PDB entry 4A4I
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 LEU 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL* 1.3 86.5 - - - +
29A ARG* 1.3 59.2 + - - +
51A ARG* 4.1 14.6 - - - +
52A GLU* 3.4 27.8 - - + +
86A THR* 3.2 8.6 - - - +
87A PHE* 2.9 67.0 + - + +
88A LYS* 5.1 2.9 - - - -
89A LYS* 4.6 17.5 - - + +
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Residues in contact with ARG 29 (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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28A LEU* 1.3 74.6 - - - +
30A GLY* 1.3 62.3 + - - +
31A THR* 6.4 0.4 - - + -
51A ARG 3.8 0.2 - - - -
52A GLU* 2.8 67.3 + - - +
53A GLY* 3.7 20.1 - - - +
85A PHE 3.3 11.9 - - - +
86A THR* 4.7 8.1 - - + -
87A PHE* 3.5 11.7 - - - -
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Residues in contact with GLY 30 (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 ARG* 1.3 78.5 - - - +
31A THR* 1.3 69.4 + - - +
48A MET* 4.0 3.8 - - - -
50A ASN* 3.1 14.6 - - - -
51A ARG* 4.3 0.4 - - - -
52A GLU 4.5 0.7 - - - -
53A GLY 5.8 0.2 - - - -
84A GLU* 3.7 0.3 - - - +
85A PHE* 3.0 47.5 + - - +
87A PHE* 3.9 2.4 - - - -
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Residues in contact with THR 31 (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 ARG* 6.3 1.3 - - + +
30A GLY* 1.3 82.6 - - - +
32A GLY* 1.3 60.9 + - - +
48A MET* 3.6 3.1 - - - -
49A ILE* 3.0 24.1 + - - +
50A ASN* 2.8 35.0 + - + +
83A VAL 3.5 9.9 - - - -
84A GLU* 4.0 22.0 - - + +
85A PHE* 3.6 7.3 - - - -
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Residues in contact with GLY 32 (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 THR* 1.3 76.4 + - - +
33A HIS* 1.3 78.0 + - - -
47A SER 3.3 13.0 - - - -
49A ILE* 3.8 11.7 - - - -
82A PRO* 3.5 3.3 - - - +
83A VAL* 2.8 30.7 + - - +
85A PHE* 3.9 2.3 - - - -
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Residues in contact with HIS 33 (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 GLY* 1.3 88.1 - - - -
34A CYS* 1.3 65.4 + - - +
46A ILE* 3.5 1.1 - - - +
47A SER* 2.8 35.5 + - - +
49A ILE* 3.8 13.3 - - + +
80A GLY* 3.4 25.4 - - - +
81A GLU 3.2 8.1 - - - +
82A PRO* 3.6 23.9 - - + +
83A VAL* 3.8 8.3 - - - +
102B PRO 3.9 7.8 + - - -
103B GLY* 3.3 30.2 + - - -
105B SER* 3.6 35.8 - - - -
106B PRO* 5.2 0.4 - - + +
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Residues in contact with CYS 34 (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 HIS* 1.3 72.1 - - - +
35A LYS* 1.3 61.9 + - - +
36A TRP* 3.5 31.6 - - - -
37A PHE* 4.0 1.8 - - - -
45A PHE 4.0 4.7 - - - -
46A ILE* 4.3 5.8 - - - +
77A LEU* 3.8 33.9 - - + -
78A LYS 3.3 26.9 - - - +
79A GLU* 3.9 4.7 - - - -
80A GLY* 2.8 27.3 + - - +
81A GLU* 2.8 14.0 + - + +
83A VAL* 4.1 4.0 - - - +
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A HIS 3.2 3.2 + - - -
34A CYS* 1.3 74.7 - - - +
36A TRP* 1.3 78.1 + - + +
45A PHE* 2.8 23.6 + - + +
47A SER* 3.4 23.9 + - - +
61A ASP* 3.4 26.9 + - - +
79A GLU* 3.7 16.5 - - - +
72B GLU* 3.2 21.2 + - - +
106B PRO* 5.7 6.1 - - - +
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Residues in contact with TRP 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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34A CYS* 3.5 9.0 - - - -
35A LYS* 1.3 100.5 - - + +
37A PHE* 1.3 74.9 + - - +
38A ASN* 3.8 23.6 - - + -
41A MET* 4.0 12.3 - - + -
43A PHE* 3.6 37.7 - + - -
44A GLY* 3.3 4.9 - - - -
45A PHE* 3.0 67.1 + + + +
64A VAL* 5.2 0.2 - - - +
79A GLU* 3.9 18.2 - - - +
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Residues in contact with PHE 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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34A CYS* 4.0 6.6 - - - -
36A TRP* 1.3 80.0 - - - +
38A ASN* 1.3 69.0 + - - +
39A VAL* 3.8 12.4 + - + +
42A GLY* 3.7 9.6 - - - -
43A PHE* 3.6 25.1 - - - -
44A GLY* 3.7 9.6 - - - -
64A VAL* 3.6 29.4 - - + -
66A GLN* 3.9 16.8 - - + -
69A LEU* 4.1 16.2 - - + -
75A ARG 4.3 3.6 - - - -
76A SER* 3.8 20.0 - - - -
77A LEU* 3.5 41.6 - - + +
79A GLU* 4.6 6.2 + - - +
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Residues in contact with ASN 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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36A TRP* 3.8 22.1 - - + -
37A PHE* 1.3 75.4 - - - +
39A VAL* 1.3 51.9 + - - +
40A ARG* 3.1 40.9 + - - +
41A MET* 2.9 49.5 + - - +
42A GLY* 2.7 31.0 + - - -
43A PHE 2.9 15.9 + - - +
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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