Contacts of the strand formed by residues 38 - 42 (chain A) in PDB entry 3CMM
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 ASN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 1.3 74.0 - - - +
39A VAL* 1.3 61.6 + - - +
61A LYS* 3.2 35.0 + - - +
62A SER* 2.4 37.8 + - - +
122A GLN* 4.1 12.0 - - + +
123A PHE* 3.7 17.6 - - + -
124A GLN* 2.7 47.4 + - - +
125A VAL 3.3 5.5 + - - -
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Residues in contact with VAL 39 (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 SER 4.5 0.2 - - - +
38A ASN* 1.3 77.9 - - - +
40A LEU* 1.3 70.6 + - - +
41A ILE* 4.2 7.9 - - + -
55A VAL* 4.2 1.6 - - + -
60A VAL* 4.0 32.1 - - + -
62A SER* 3.1 8.4 + - - +
63A MET* 3.7 22.5 - - + -
64A THR* 2.8 29.5 + - - +
123A PHE* 4.0 3.3 - - - -
125A VAL* 3.5 12.1 - - + +
127A VAL* 4.5 6.1 - - + -
374A VAL* 4.2 25.6 - - + -
378A CYS* 4.5 10.3 - - - -
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Residues in contact with LEU 40 (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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39A VAL* 1.3 74.4 - - - +
41A ILE* 1.3 71.7 + - - +
42A LEU* 3.5 30.5 - - + -
64A THR* 3.3 30.7 - - + +
65A VAL 4.0 1.8 - - - +
66A PHE* 4.4 7.6 - - + -
111A LEU* 4.4 5.6 - - + -
114A LEU* 4.9 1.8 - - + -
120A LEU* 4.7 14.4 - - + -
123A PHE* 3.8 35.0 - - + -
125A VAL 2.9 10.9 + - - +
126A VAL* 3.4 24.7 - - + +
127A VAL* 2.9 26.9 + - - +
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Residues in contact with ILE 41 (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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39A VAL* 4.4 4.5 - - + -
40A LEU* 1.3 79.0 - - - +
42A LEU* 1.3 64.2 + - - +
43A GLY 3.7 19.4 + - - +
44A LEU* 4.0 4.9 - - + +
48A GLY* 4.1 14.8 - - - +
51A ILE* 3.8 14.1 - - + -
52A ALA* 3.6 40.2 - - + +
63A MET* 3.7 20.2 - - + -
64A THR 2.9 10.6 + - - +
65A VAL* 3.6 6.9 - - + -
66A PHE 3.1 24.8 + - - -
127A VAL* 3.6 24.5 - - + +
129A THR* 4.4 5.2 - - - +
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Residues in contact with LEU 42 (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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40A LEU* 3.5 26.2 - - + -
41A ILE* 1.3 69.7 - - - +
43A GLY* 1.3 61.4 + - - +
66A PHE* 3.6 34.3 - - + -
114A LEU* 3.9 14.1 - - + -
126A VAL* 4.0 19.3 - - + -
127A VAL 2.8 17.9 + - - +
128A ALA* 4.2 9.6 - - + -
129A THR* 2.8 30.0 + - - +
131A THR* 3.7 3.8 + - - -
132A VAL* 3.8 16.1 - - + +
140A ILE* 3.9 29.6 - - + -
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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