Contacts of the strand formed by residues 28 - 37 (chain A) in PDB entry 4MSP
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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26A GLY 3.7 1.3 + - - +
27A ASP* 1.3 74.7 - - - +
29A MET* 1.3 60.5 + - - +
57A TRP* 3.9 30.7 - - + -
58A PHE 3.7 3.1 - - - +
59A THR* 3.4 29.8 - - + +
114A GLU 3.8 0.2 - - - +
115A ILE* 3.3 6.8 - - - +
116A ARG* 2.8 48.5 + - + +
117A ASN 3.7 19.5 - - - +
118A GLY* 4.3 10.3 - - - +
119A PRO* 4.5 9.9 - - + -
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Residues in contact with MET 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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23A THR* 3.8 31.2 - - + -
27A ASP* 4.5 7.9 - - + +
28A LEU* 1.3 76.0 - - - +
30A LEU* 1.3 60.8 + - - +
31A VAL* 3.7 13.8 + - + +
56A ILE 3.4 2.3 - - - +
57A TRP* 3.3 5.4 - - - -
58A PHE* 2.7 57.1 + - + +
60A LEU* 3.9 22.2 - - + -
73A LEU* 3.9 31.2 - - + +
76A MET* 3.9 14.6 - - - -
112A LEU* 3.7 20.6 - - + -
114A GLU 3.6 3.8 - - - -
115A ILE* 5.2 0.7 - - + -
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Residues in contact with LEU 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 MET* 1.3 72.1 - - - +
31A VAL* 1.3 61.1 + - - +
55A PRO* 3.7 38.1 - - + +
56A ILE 3.7 19.3 - - - +
57A TRP* 3.6 40.5 - - + +
112A LEU* 3.5 1.2 - - - +
113A LEU* 2.8 44.7 + - + +
114A GLU* 2.9 33.4 + - + +
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Residues in contact with VAL 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 MET* 4.0 20.6 - - + +
30A LEU* 1.3 80.3 - - - +
32A HIS* 1.3 63.7 + - - +
33A TYR* 4.5 0.2 - - + -
47A THR* 4.5 0.2 + - - -
55A PRO* 3.4 7.3 - - - +
56A ILE* 2.9 60.8 + - + +
58A PHE* 4.9 3.1 - - + -
69A TRP* 4.1 21.3 - - + -
73A LEU* 5.7 0.2 - - + -
110A ILE* 3.8 19.5 - - + -
111A ASP 3.1 12.8 - - - +
112A LEU* 3.8 17.3 - - + -
113A LEU* 4.6 0.7 - - - +
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Residues in contact with HIS 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 VAL* 1.3 74.2 - - - +
33A TYR* 1.3 62.8 + - - +
47A THR* 2.7 22.9 + - - +
48A HIS* 3.4 40.1 + + + +
53A GLY 3.1 28.8 + - - -
54A GLN 3.8 1.6 - - - -
55A PRO* 3.4 23.2 - - + +
110A ILE* 3.4 2.4 - - - +
111A ASP* 2.9 36.0 + - + +
113A LEU* 3.8 27.5 - - + +
208A PGO 3.4 9.8 + - + +
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Residues in contact with TYR 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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31A VAL* 4.5 0.9 - - + -
32A HIS* 1.3 76.5 - - - +
34A GLU* 1.3 70.4 + - - +
35A GLY 4.4 0.9 - - - -
44A PHE* 5.0 1.7 - + - -
45A HIS* 3.3 41.6 + + + +
46A SER* 3.5 0.9 - - - -
47A THR* 2.9 54.7 + - + -
48A HIS* 4.9 0.4 - - - -
56A ILE* 4.0 18.8 - - + -
69A TRP* 3.5 26.2 - + + -
108A PHE* 3.6 30.7 - + - -
109A ASN 3.1 13.2 - - - +
110A ILE* 3.8 16.2 - - + -
208A PGO 3.5 2.9 - - - -
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Residues in contact with GLU 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 TYR* 1.3 78.4 - - - +
35A GLY* 1.3 59.7 + - - +
36A TYR* 3.4 33.4 + - + +
43A LEU* 3.9 8.3 - - + +
45A HIS 3.3 3.8 - - - -
46A SER* 3.5 29.0 + - - +
48A HIS* 4.4 8.9 - - + +
49A LYS* 5.5 4.2 + - - -
107A ILE 3.7 0.9 - - - +
108A PHE* 3.2 5.4 - - - +
109A ASN* 3.0 38.7 + - + +
208A PGO 4.0 23.9 + - - +
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Residues in contact with GLY 35 (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 TYR* 4.0 1.8 - - - -
34A GLU* 1.3 75.4 - - - +
36A TYR* 1.3 55.9 + - - -
43A LEU* 3.5 5.4 - - - +
44A PHE* 2.7 57.0 + - - -
45A HIS 2.8 12.5 + - - -
107A ILE 3.4 5.4 - - - -
108A PHE* 3.9 7.6 - - - -
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Residues in contact with TYR 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 GLU* 3.4 42.3 + - + -
35A GLY* 1.3 73.4 - - - -
37A LEU* 1.3 65.2 + - - +
41A GLY* 3.4 22.9 - - - +
42A SER 3.1 6.7 - - - +
43A LEU* 3.6 31.2 - - + +
44A PHE* 3.3 12.8 - - - -
106A LEU* 3.5 1.7 - - - -
107A ILE* 2.7 58.6 + - + +
109A ASN* 3.7 20.9 + - - -
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Residues in contact with LEU 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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36A TYR* 1.3 74.2 - - - +
38A GLU* 1.3 58.6 + - - +
39A LYS* 4.3 13.0 - - + +
40A ASP* 3.5 18.4 - - - +
41A GLY* 2.8 31.0 + - - -
42A SER* 2.8 23.4 + - - +
44A PHE* 4.1 8.5 - - + -
99A LYS 5.0 2.9 - - - +
100A ILE* 4.0 19.5 - - + -
101A PRO* 3.9 24.7 - - + -
104A SER* 4.0 17.3 - - - +
105A THR 3.9 2.0 - - - +
106A LEU* 4.0 22.4 - - + -
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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