Contacts of the strand formed by residues 28 - 37 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY 3.6 15.0 - - - +
27B ASP* 1.3 72.9 - - - +
29B MET* 1.3 61.4 + - - +
57B TRP* 3.9 18.4 - - + -
58B PHE 3.6 5.4 - - - +
59B THR* 3.9 23.8 - - + +
114B GLU 3.7 0.7 - - - +
115B ILE* 3.4 6.1 - - - +
116B ARG* 2.7 43.8 + - + +
117B ASN* 5.3 2.9 - - - -
118B GLY 5.7 2.2 - - - +
207B PGO 3.6 40.4 - - + +
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B THR* 3.7 34.1 - - + -
27B ASP* 4.1 7.9 - - + +
28B LEU* 1.3 77.8 - - - +
30B LEU* 1.3 62.0 + - - +
31B VAL* 3.5 11.1 + - + +
56B ILE 3.4 2.8 - - - +
57B TRP* 3.4 3.6 - - - -
58B PHE* 2.7 51.8 + - + +
60B LEU* 3.8 23.6 - - + -
73B LEU* 3.8 29.6 - - + +
76B MET* 3.9 17.9 - - - -
112B LEU* 3.7 18.2 - - + -
114B GLU 3.5 4.9 - - - -
115B ILE* 5.3 0.2 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET* 1.3 71.8 - - - +
31B VAL* 1.3 58.2 + - - +
55B PRO* 3.8 32.3 - - + +
56B ILE 3.6 21.1 - - - +
57B TRP* 3.6 47.8 - - + +
112B LEU* 3.6 2.8 - - - +
113B LEU* 2.8 43.7 + - + +
114B GLU* 2.9 28.3 + - + +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET* 4.2 19.7 - - + +
30B LEU* 1.3 80.3 - - - +
32B HIS* 1.3 64.3 + - - +
33B TYR* 4.4 4.5 - - + -
47B THR* 4.4 0.3 - - - +
55B PRO* 3.2 7.8 - - - +
56B ILE* 2.9 61.6 + - + +
58B PHE* 4.7 2.2 - - + -
69B TRP* 4.2 21.3 - - + -
73B LEU* 5.7 1.3 - - + -
110B ILE* 3.9 16.4 - - + -
111B ASP 3.2 13.0 - - - +
112B LEU* 4.0 15.9 - - + -
113B LEU* 4.4 0.4 - - - -
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 1.3 76.7 - - - +
33B TYR* 1.3 63.6 + - - +
47B THR* 2.7 22.5 + - - +
48B HIS* 3.3 39.3 + + + -
53B GLY 3.0 29.7 + - - -
54B GLN 3.6 2.5 - - - -
55B PRO* 3.4 24.3 - - + +
109B ASN 4.0 0.2 - - - +
110B ILE* 3.5 0.7 - - - -
111B ASP* 2.9 43.4 + - + +
113B LEU* 3.9 26.1 - - + +
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Residues in contact with TYR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 4.4 1.6 - - + -
32B HIS* 1.3 77.2 - - - +
34B GLU* 1.3 69.9 + - - +
35B GLY 4.5 1.1 - - - -
44B PHE* 5.2 1.1 - + - -
45B HIS* 3.2 40.8 + + + +
46B SER* 3.4 2.4 - - - -
47B THR* 3.0 50.8 + - + -
48B HIS* 5.1 1.9 + - - -
56B ILE* 4.0 18.8 - - + -
69B TRP* 3.5 24.7 - + + -
108B PHE* 3.7 32.1 - + - -
109B ASN 3.1 12.6 - - - +
110B ILE* 3.7 16.2 - - + -
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 1.3 82.3 - - - +
35B GLY* 1.3 59.7 + - - +
36B TYR* 2.8 37.4 + - + +
43B LEU* 4.0 4.0 - - + -
45B HIS 3.3 4.7 - - - -
46B SER* 3.8 21.2 + - - +
48B HIS* 4.4 14.8 + - + +
107B ILE 3.8 0.5 - - - +
108B PHE* 3.3 6.4 - - - -
109B ASN* 2.9 51.4 + - + +
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Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 4.1 1.6 - - - -
34B GLU* 1.3 74.7 - - - +
36B TYR* 1.3 57.0 + - - -
43B LEU* 3.4 5.0 - - - +
44B PHE* 2.8 55.8 + - - -
45B HIS 2.7 15.7 + - - -
107B ILE 3.5 4.9 - - - -
108B PHE* 3.8 8.3 - - - -
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLU* 2.8 45.4 + - + -
35B GLY* 1.3 74.6 - - - -
37B LEU* 1.3 65.7 + - - +
41B GLY* 3.5 22.7 - - - +
42B SER 3.2 6.3 - - - +
43B LEU* 3.7 31.5 - - + +
44B PHE* 3.2 12.6 - - - -
106B LEU* 3.5 1.7 - - - -
107B ILE* 2.8 53.9 + - + +
109B ASN* 4.9 7.9 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 1.3 73.6 - - - +
38B GLU* 1.3 58.8 + - - +
39B LYS* 4.2 9.6 - - + +
40B ASP* 3.5 20.2 - - - +
41B GLY* 2.9 31.4 + - - -
42B SER* 2.9 25.4 + - - +
44B PHE* 3.8 21.5 - - + -
99B LYS 4.0 8.1 - - - +
100B ILE* 4.0 7.4 - - + -
101B PRO* 3.6 38.8 - - + -
104B SER* 4.1 7.2 - - - +
105B THR 4.0 1.6 - - - +
106B LEU* 4.0 17.5 - - + -
107B ILE* 5.2 0.2 - - - +
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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