Contacts of the strand formed by residues 23 - 32 (chain A) in PDB entry 3FEV
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 LEU 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A LEU* 3.5 7.7 - - - +
3A CYS* 3.6 2.8 - - - -
17A CYS* 4.4 0.5 - - - -
22A ASN* 1.3 85.5 - - - +
24A CYS* 1.3 63.1 + - - +
42A CYS* 3.4 5.7 - - - +
43A ALA* 2.8 39.3 + - + +
44A ALA 4.1 4.9 - - - +
45A THR* 3.6 36.3 - - - -
46A CYS* 3.6 15.7 - - + +
57A CYS* 4.3 9.2 - - + -
58A CYS* 3.4 20.9 - - - +
59A GLY* 4.4 2.9 - - - -
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Residues in contact with CYS 24 (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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1A LEU* 3.8 8.1 - - - -
2A THR 3.8 7.0 - - - -
3A CYS* 2.1 48.5 - - - -
23A LEU* 1.3 73.9 - - - +
25A PHE* 1.3 60.8 + - - +
41A GLY 3.2 5.2 - - - -
57A CYS* 3.1 7.1 - - - +
58A CYS* 2.8 30.9 + - - +
60A THR 4.0 3.4 - - - -
63A CYS* 3.7 26.0 - - - -
64A ASN* 3.5 22.4 - - + -
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Residues in contact with PHE 25 (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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24A CYS* 1.3 74.8 - - - +
26A LYS* 1.3 75.3 + - - +
27A ARG* 3.8 9.6 - - + -
39A THR* 3.5 26.5 - - - -
40A ARG* 3.2 26.7 - - - +
41A GLY* 2.8 47.4 + - - -
42A CYS 3.4 20.0 - - - -
43A ALA* 4.1 10.3 - - + -
55A ILE* 4.8 5.4 - - + -
56A ASN 3.3 9.9 - - - +
57A CYS* 4.1 13.7 - - - -
58A CYS* 5.9 0.2 - - - -
64A ASN* 3.0 21.6 + - - -
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Residues in contact with LYS 26 (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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25A PHE* 1.3 79.2 - - - +
27A ARG* 1.3 61.1 + - - +
28A TRP* 3.9 25.8 - - + -
38A PHE* 3.9 20.9 - - + -
39A THR 3.5 6.7 - - - -
40A ARG* 4.3 5.2 - - + +
55A ILE* 3.4 4.2 - - - +
56A ASN* 2.8 59.7 + - - +
57A CYS 5.9 0.2 - - - -
58A CYS* 5.3 5.3 - - - -
63A CYS 5.0 3.5 + - - -
64A ASN* 3.8 35.4 - - + +
65A LYS* 5.1 3.8 - - - +
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Residues in contact with ARG 27 (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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25A PHE* 4.0 11.7 - - + -
26A LYS* 1.3 75.8 - - - +
28A TRP* 1.3 70.5 + - - +
29A GLN* 3.5 38.6 + - + +
37A ASP 3.6 1.2 - - - +
38A PHE* 3.4 8.1 - - - -
39A THR* 2.8 55.2 + - - +
53A ASP* 2.8 27.7 + - - -
54A VAL 3.3 4.3 - - - +
55A ILE* 3.7 29.2 - - + +
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Residues in contact with TRP 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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26A LYS* 3.9 39.7 - - + -
27A ARG* 1.3 76.7 - - - +
29A GLN* 1.3 60.2 + - - +
36A TYR* 3.8 28.4 - + + -
37A ASP 3.6 3.4 - - - -
38A PHE* 3.4 32.8 - + + -
53A ASP* 3.3 10.2 - - - +
54A VAL* 2.8 61.9 + - + +
56A ASN* 3.8 23.1 - - - -
13B THR* 5.0 8.7 - - + +
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Residues in contact with GLN 29 (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 ARG* 3.5 40.3 + - + +
28A TRP* 1.3 71.2 - - - +
30A TYR* 1.3 72.9 + - - +
31A ILE* 3.4 22.9 + - + +
36A TYR* 3.3 5.6 - - - -
37A ASP* 2.8 55.6 + - + +
53A ASP* 3.5 7.0 - - - +
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Residues in contact with TYR 30 (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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29A GLN* 1.3 80.8 + - - +
31A ILE* 1.3 66.4 + - - +
32A SER* 3.4 30.3 - - - -
33A PRO* 3.0 34.0 - - + +
35A MET 4.1 0.4 - - - -
36A TYR* 3.6 34.1 - + + -
52A ARG* 3.4 69.8 + - + +
53A ASP* 3.0 12.0 + - - +
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Residues in contact with ILE 31 (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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29A GLN* 3.5 43.3 - - - +
30A TYR* 1.3 82.1 - - - +
32A SER* 1.3 63.1 + - - +
35A MET* 2.9 45.3 + - + +
36A TYR 4.6 0.9 - - - -
37A ASP* 4.0 17.0 - - + +
14B THR* 5.3 1.6 - - - +
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Residues in contact with SER 32 (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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30A TYR* 3.4 19.0 - - - -
31A ILE* 1.3 78.8 - - - +
33A PRO* 1.4 77.9 - - - +
34A ARG* 3.0 6.9 + - - +
35A MET* 3.0 44.6 + - - +
36A TYR* 5.3 0.5 - - - -
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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