Contacts of the strand formed by residues 40 - 47 (chain M) in PDB entry 6E0P
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 VAL 40 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32M GLU* 3.3 23.3 - - - +
34M VAL* 3.8 25.8 - - + -
39M SER* 1.3 81.1 - - - +
41M LYS* 1.3 65.7 + - - +
42M MET* 3.8 27.6 - - + +
103M MET 3.1 5.5 - - - +
104M GLU* 3.3 2.8 - - - -
105M LEU* 3.0 36.9 + - + +
108M LEU* 3.8 22.0 - - + +
138M VAL* 4.4 12.1 - - + -
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Residues in contact with LYS 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLU* 4.9 5.2 - - - +
39M SER 4.3 0.8 + - - -
40M VAL* 1.3 74.7 - - - +
42M MET* 1.3 58.3 + - - +
43M PRO* 4.1 5.0 - - - +
102M TYR* 3.8 33.3 - - + -
103M MET 3.3 2.9 - - - -
104M GLU* 3.3 38.2 + - + +
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Residues in contact with MET 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M GLN* 4.6 0.9 - - - +
29M SER* 4.2 11.0 - - - +
32M GLU* 5.5 2.7 - - - +
40M VAL* 3.8 14.8 - - + -
41M LYS* 1.3 73.6 - - - +
43M PRO* 1.3 69.1 - - + +
58M TRP* 4.1 22.6 - - + -
101M VAL 3.7 0.5 - - - +
102M TYR* 3.3 6.2 - - - -
103M MET* 3.1 34.8 + - + +
105M LEU* 3.8 26.7 - - + -
116M TYR* 3.7 29.4 - - + +
136M THR* 4.2 15.7 - - + +
138M VAL* 3.7 28.5 - - + -
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Residues in contact with PRO 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M GLN 4.5 0.7 - - - +
28M GLN* 3.4 26.1 - - - +
29M SER* 3.7 30.7 - - - +
32M GLU* 5.8 1.1 - - - +
41M LYS 4.1 4.7 - - - +
42M MET* 1.3 88.1 - - - +
44M CYS* 1.3 60.0 + - - +
45M LYS* 3.8 5.6 - - + +
58M TRP* 4.4 2.4 - - - -
100M THR* 3.9 9.2 - - + -
101M VAL 3.7 4.0 - - - +
102M TYR* 3.7 23.8 - - + -
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Residues in contact with CYS 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M LEU* 3.7 21.1 - - - -
27M GLN 3.4 6.1 - - - -
43M PRO* 1.3 72.5 - - - +
45M LYS* 1.3 65.1 + - - +
46M ALA* 3.2 7.3 + - - +
56M ILE* 4.0 12.4 - - - +
58M TRP* 3.7 12.3 - - + -
99M SER 3.9 1.4 - - - +
100M THR* 4.0 0.8 - - - +
101M VAL* 2.9 34.1 + - + +
118M CYS* 2.0 48.9 - - - -
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Residues in contact with LYS 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M LEU 3.5 0.3 - - - -
27M GLN* 2.6 61.4 + - + +
43M PRO* 3.8 4.5 - - + -
44M CYS* 1.3 72.3 - - - +
46M ALA* 1.3 75.0 + - - +
47M SER* 4.3 9.7 - - - -
98M SER* 3.3 28.3 + - - +
99M SER* 3.7 4.6 - - - -
100M THR* 3.3 16.3 - - + +
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Residues in contact with ALA 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLN 3.8 4.3 - - - -
26M LEU* 4.5 9.4 - - + +
27M GLN* 4.2 0.4 - - - -
44M CYS 3.2 6.7 + - - +
45M LYS* 1.3 86.7 + - - +
47M SER* 1.3 64.5 + - - +
49M TYR* 3.3 31.9 - - + +
51M PHE* 4.1 11.7 - - + -
56M ILE* 4.6 1.8 - - + -
99M SER* 3.0 28.7 + - - +
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Residues in contact with SER 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M GLU 3.8 1.3 + - - +
24M VAL* 3.8 1.7 - - - -
25M GLN* 3.1 31.8 + - - +
27M GLN* 3.4 25.9 + - - -
45M LYS* 4.3 9.2 - - - -
46M ALA* 1.3 77.4 - - - +
48M GLY* 1.3 62.5 + - - +
49M TYR* 3.5 10.0 - - - -
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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