Contacts of the strand formed by residues 26 - 33 (chain A) in PDB entry 3CS0
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.5 7.2 - - + +
23A MSE 2.9 12.3 + - - +
24A PRO 3.6 4.2 - - - +
25A SER* 1.3 81.8 - - - +
27A VAL* 1.3 76.0 + - - +
90A GLY 3.6 11.0 - - - +
91A VAL* 4.7 4.7 - - + +
118A SER* 4.4 8.1 + - - -
150A ILE* 5.4 0.7 - - + -
167A ILE* 3.8 42.4 - - + +
168A GLY* 4.5 6.5 - - - -
175A GLU* 3.3 22.6 - - + +
212A GLY* 4.7 2.0 - - - -
213A ALA* 3.8 30.5 - - + +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A SER 4.0 0.7 - - - +
26A VAL* 1.3 83.5 - - - +
28A SER* 1.3 63.3 + - - +
29A ILE* 4.3 4.9 - - + -
89A SER* 3.2 8.7 - - - -
90A GLY* 2.8 49.1 + - - +
92A ILE* 3.7 24.7 - - + -
100A VAL* 4.0 10.5 - - + -
115A VAL* 3.9 20.9 - - + -
116A GLN 3.8 11.9 - - - +
117A LEU* 3.7 25.1 - - + -
169A ASN* 6.0 0.2 - - - -
175A GLU* 5.9 3.4 - - - -
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Residues in contact with SER 28 (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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27A VAL* 1.3 75.3 - - - +
29A ILE* 1.3 63.5 + - - +
30A ASN* 4.8 6.2 + - - -
88A GLY 3.4 7.9 - - - -
89A SER* 4.3 0.2 - - - +
114A LYS 3.9 0.5 - - - +
115A VAL* 3.6 3.1 - - - -
116A GLN* 2.9 50.2 + - - +
117A LEU 5.2 0.7 + - - -
169A ASN* 3.3 31.6 + - - -
174A GLY* 5.5 0.9 - - - -
175A GLU* 5.5 6.1 + - - +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.3 7.2 - - + -
28A SER* 1.3 79.5 - - - +
30A ASN* 1.3 67.8 + - - +
31A VAL* 4.0 23.1 - - + +
87A LEU* 3.3 8.8 - - - +
88A GLY 2.7 38.9 + - - +
89A SER 3.3 28.0 - - - +
90A GLY* 4.0 5.4 - - - +
100A VAL* 4.7 0.4 - - + -
102A THR* 3.8 17.9 - - + +
106A VAL* 4.7 7.9 - - + -
107A VAL* 5.5 2.9 - - + -
113A ILE* 4.7 13.0 - - + -
114A LYS 3.6 5.6 - - - +
115A VAL* 4.4 7.2 - - + -
139A ILE* 3.8 21.8 - - + -
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Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A SER* 4.8 8.1 + - - -
29A ILE* 1.3 81.3 - - - +
31A VAL* 1.3 62.8 + - - +
86A ALA 3.7 3.2 - - - +
87A LEU* 3.9 16.8 - - - +
112A VAL* 3.9 1.6 - - - +
113A ILE* 3.4 3.8 - - - +
114A LYS* 2.8 52.8 + - + +
116A GLN* 4.6 18.0 - - - +
122A LYS* 5.0 7.9 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ILE* 4.0 17.3 - - + -
30A ASN* 1.3 80.5 - - - +
32A GLU* 1.3 69.4 - - - +
84A PHE* 3.9 18.4 - - + -
85A MSE 3.3 8.5 - - - +
86A ALA* 2.9 35.7 + - + +
106A VAL* 3.7 25.1 - - + +
107A VAL* 4.0 11.9 - - + -
110A ALA* 3.3 23.6 - - + -
112A VAL* 3.4 2.7 - - - -
113A ILE* 4.1 12.8 - - + -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 1.3 78.7 - - - +
33A GLY* 1.3 51.3 + - - +
83A LYS* 3.6 33.2 + - - -
84A PHE 3.5 2.9 - - - -
85A MSE 4.3 12.3 - - + -
110A ALA 3.6 0.3 - - - -
111A THR* 2.7 33.9 + - - -
112A VAL* 2.8 43.2 + - + +
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Residues in contact with GLY 33 (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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32A GLU* 1.3 75.5 - - - +
34A SER* 1.3 66.1 + - - -
83A LYS* 3.6 8.9 - - - +
84A PHE* 2.9 48.1 + - - +
109A ASN 3.4 10.3 - - - -
111A THR* 3.7 9.4 - - - -
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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