Contacts of the strand formed by residues 44 - 48 (chain M) in PDB entry 1V7M
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 44 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I LEU 4.1 17.7 + - - +
105I TYR* 4.8 2.4 - - - +
106I TRP* 4.3 24.5 + - - +
35M PHE* 2.9 10.7 - - - -
36M GLN* 2.8 38.7 + - + +
42M SER* 4.2 11.2 - - - +
43M PRO* 1.3 90.8 - - - +
45M LEU* 1.3 68.2 + - - +
46M TRP* 4.1 12.5 - - + +
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Residues in contact with LEU 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I SER 5.7 1.1 - - - +
103I PHE 3.8 19.3 + - - +
104I LEU* 4.0 34.2 + - + +
106I TRP* 4.7 2.0 - - - +
33M TYR* 5.1 0.7 - - + -
34M TRP 3.7 16.8 - - - +
35M PHE* 3.6 21.4 - - + -
44M LYS* 1.3 75.2 - - - +
46M TRP* 1.3 68.0 + - - +
47M ILE 3.8 13.5 - - - +
48M TYR* 4.0 31.0 - - + -
54M ALA* 3.3 19.2 - - + +
55M SER 4.9 2.4 - - - +
57M VAL* 4.5 0.5 - - - +
90M ARG* 4.8 9.4 - - - +
113X PRO* 4.1 9.6 - - + -
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Residues in contact with TRP 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M TRP* 2.7 23.7 + - + +
35M PHE* 3.9 8.3 - - - +
36M GLN* 3.3 52.7 - - + -
44M LYS* 4.6 8.5 - - + -
45M LEU* 1.3 83.5 - - - +
47M ILE* 1.3 75.2 + - + +
53M LEU* 3.7 1.7 - - - -
54M ALA* 2.8 29.0 + - - -
55M SER 5.9 0.4 - - - -
56M GLY 4.6 10.8 - - - -
57M VAL* 3.3 34.5 - - + +
58M PRO* 4.4 5.8 - - + -
61M PHE* 3.3 44.7 - + - -
72M LEU* 4.0 12.1 - - + -
81M ASP* 5.3 1.1 - - - -
85M TYR* 3.7 11.6 - + - -
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Residues in contact with ILE 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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32M MET 5.2 0.2 - - - +
33M TYR* 3.4 3.0 - - - -
34M TRP* 2.7 46.1 + - + +
45M LEU* 3.8 3.9 - - - +
46M TRP* 1.3 98.0 - - + +
48M TYR* 1.3 65.2 + - - +
50M THR 3.4 29.2 - - - +
51M SER* 4.1 3.8 - - - +
52M ASN 3.3 13.7 - - - +
53M LEU* 4.4 12.8 - - + -
54M ALA 4.6 0.2 - - - +
61M PHE* 5.1 1.6 - - + -
62M ARG 4.1 4.3 - - - +
63M GLY* 3.8 24.2 - - - +
72M LEU* 3.3 31.0 - - + -
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Residues in contact with TYR 48 (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 MET 4.4 0.9 - - - -
33M TYR* 3.8 20.9 - - + -
45M LEU* 4.0 23.1 - - + -
47M ILE* 1.3 74.2 - - - +
49M SER* 1.3 78.4 + - - +
50M THR 3.1 3.5 + - - -
51M SER 3.3 0.6 + - - -
52M ASN* 2.9 69.2 + - + +
53M LEU 3.7 14.8 + - - -
54M ALA* 4.1 10.3 - - + -
55M SER 5.4 0.4 - - - -
90M ARG* 6.0 0.2 - - - +
112X LEU* 4.8 4.7 - - + -
113X PRO* 3.7 39.5 - - + +
114X PRO 4.7 1.4 + - - -
115X GLN* 3.6 33.3 + - + +
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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