Contacts of the strand formed by residues 43 - 50 (chain A) in PDB entry 7CMO
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.3 6.4 - - - -
39A ALA* 2.8 31.7 + - + -
40A ASP* 3.1 24.0 + - + +
41A LYS 3.8 9.9 - - - +
42A ASP* 1.3 85.3 - - + +
44A PHE* 1.3 62.1 + - - +
137A GLY* 3.7 14.4 - - - -
138A VAL 3.4 24.7 - - - +
139A LYS* 5.5 1.6 - - + -
161A VAL* 3.9 26.9 - - + -
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Residues in contact with PHE 44 (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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37A ILE* 3.2 32.5 - - + +
38A TYR* 3.7 31.9 - + - -
42A ASP* 4.7 7.9 - - - -
43A VAL* 1.3 77.6 - - - +
45A HIS* 1.3 70.4 + - - +
46A MET 3.6 0.2 + - - -
97A ILE* 4.0 16.4 - - + -
137A GLY* 3.2 5.4 - - - -
138A VAL* 2.8 47.2 + - + +
140A VAL* 3.6 15.0 - - + -
217A ILE* 3.6 36.6 - - + -
220A ILE* 3.6 24.7 - - + -
221A LYS* 6.3 0.2 - - + -
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Residues in contact with HIS 45 (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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4A PHE* 3.9 23.4 - + - -
35A ILE* 3.1 24.7 - - + +
36A PRO* 2.8 40.1 + - + +
37A ILE 2.7 9.8 + - - +
39A ALA* 3.2 37.7 - - + +
43A VAL 4.1 0.6 + - - -
44A PHE* 1.3 73.6 - - - +
46A MET* 1.3 59.1 + - - +
97A ILE* 3.7 15.1 - - - +
98A PRO* 3.0 22.1 - - + +
135A ILE* 4.3 8.5 - - + -
136A ILE 3.2 12.1 - - - +
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Residues in contact with MET 46 (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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45A HIS* 1.3 74.2 - - - +
47A VAL* 1.3 70.3 + - - +
48A VAL* 3.7 13.5 + - + +
93A ASN 3.2 29.4 - - - +
94A TYR 3.6 3.4 - - - +
95A GLY* 3.4 25.4 - - - +
96A ALA 3.5 10.5 - - - +
97A ILE* 4.8 1.3 - - + -
122A VAL* 3.7 27.4 - - + +
124A GLU* 3.8 18.8 - - + -
135A ILE* 3.5 5.0 - - - +
136A ILE* 2.9 45.7 + - + +
138A VAL* 3.9 21.3 - - + -
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Residues in contact with VAL 47 (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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21A LEU* 5.1 1.6 - - + -
31A PRO* 4.0 24.9 - - + +
35A ILE* 3.6 30.3 - - + -
46A MET* 1.3 72.7 - - - +
48A VAL* 1.3 62.2 + - - +
49A GLU* 3.5 2.1 + - + +
60A ILE* 4.4 13.5 - - + -
69A ILE* 4.1 25.6 - - + -
95A GLY* 3.2 3.1 - - - -
96A ALA 2.9 37.2 + - - +
98A PRO* 4.3 8.9 - - + +
133A GLY* 4.9 2.9 - - - -
134A GLU 4.0 2.2 - - - +
135A ILE* 3.7 17.7 - - + -
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Residues in contact with VAL 48 (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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46A MET* 4.0 11.4 - - + -
47A VAL* 1.3 71.9 - - - +
49A GLU* 1.3 61.6 + - - +
50A VAL 3.7 23.8 - - - +
51A PRO 4.5 1.3 - - - -
69A ILE* 4.0 3.6 - - - +
93A ASN* 4.4 6.7 - - + -
94A TYR 3.9 6.3 - - - +
130A CYS* 4.1 20.4 - - + +
131A ALA 3.7 17.7 - - - +
132A ARG* 3.9 0.2 - - - -
133A GLY* 3.1 25.8 + - - -
134A GLU 3.2 19.6 + - - +
136A ILE* 3.7 31.4 - - + -
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Residues in contact with GLU 49 (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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47A VAL 3.5 4.9 + - - +
48A VAL* 1.3 75.7 - - - +
50A VAL* 1.3 63.3 + - + +
51A PRO* 4.7 0.2 - - - -
58A MET* 3.2 37.3 - - - +
59A GLU* 3.6 18.9 - - - +
60A ILE* 3.2 36.5 + - + +
69A ILE* 4.3 9.0 - - + -
94A TYR* 2.9 25.5 + - + +
95A GLY* 3.5 28.3 - - - +
96A ALA* 4.0 8.8 - - - +
119A PRO* 5.6 0.9 - - - +
121A ASP* 4.3 5.0 - - - +
132A ARG* 3.5 16.1 - - - +
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Residues in contact with VAL 50 (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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48A VAL* 3.7 4.6 - - - +
49A GLU* 1.3 84.7 - - + +
51A PRO* 1.3 66.5 - - - +
54A SER* 3.7 11.7 - - - +
56A ALA 3.5 20.2 - - - +
58A MET* 3.5 24.9 - - + +
90A TYR* 3.3 33.7 - - + +
93A ASN* 3.7 2.8 - - - -
94A TYR* 3.1 46.9 + - + +
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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