Contacts of the strand formed by residues 40 - 48 (chain C) in PDB entry 4B2B
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 HIS 40 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C SER* 2.7 29.0 + - - +
33C LEU 3.6 5.4 - - - -
34C ASN* 3.5 5.8 - - - +
39C TYR* 1.3 84.8 - - - +
41C PHE* 1.3 60.6 + - - +
42C CYS 3.1 31.9 + - - -
43C GLY* 4.1 1.8 - - - -
73C ILE* 3.7 25.8 - - + -
141C TRP* 3.8 41.5 - + + +
193C GLY* 2.9 24.4 + - - -
47D LEU* 3.5 21.6 - - + +
49D TYR* 4.7 2.2 + - - -
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.0 48.2 + - + -
34C ASN 3.7 2.9 - - - -
37C SER* 3.3 35.2 - - - -
39C TYR* 3.3 11.9 + - + -
40C HIS* 1.3 79.6 - - - +
42C CYS* 1.4 85.8 + - + +
58C CYS* 3.2 28.7 - - + -
60C LYS* 3.6 26.9 - - + +
63C ILE* 3.9 15.7 - - + -
193C GLY* 4.2 2.0 - - - -
46D ASP* 3.7 3.1 - - + -
47D LEU* 3.0 46.8 + - - +
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Residues in contact with CYS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 2.8 29.3 + - + -
40C HIS* 3.1 14.7 - - - -
41C PHE* 1.4 99.4 - - + +
43C GLY* 1.3 65.3 + - - +
58C CYS* 2.1 53.8 - - + -
193C GLY 4.2 5.6 - - - -
195C ALA 3.2 5.6 - - - +
46D ASP* 3.5 19.3 - - - -
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLN* 3.9 11.0 - - - -
31C VAL 3.4 12.1 - - - -
33C LEU* 3.7 6.6 - - - +
40C HIS* 4.1 5.0 - - - -
42C CYS* 1.3 75.9 - - - +
44C GLY* 1.3 52.6 + - - -
54C SER* 2.8 28.1 + - - -
193C GLY 4.2 3.6 + - - -
194C ASP 4.3 2.1 + - - -
195C ALA 2.7 12.2 + - - -
196C GLY* 3.2 11.2 - - - -
197C GLY* 3.9 4.5 - - - -
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLN* 3.7 8.3 + - - -
31C VAL* 3.0 43.3 + - - +
33C LEU* 5.0 0.4 - - - -
43C GLY* 1.3 74.3 - - - -
45C SER* 1.3 64.0 + - - -
52C VAL* 4.1 4.5 - - - -
53C VAL 3.3 7.4 - - - -
54C SER* 4.2 1.1 - - - -
196C GLY 3.3 11.6 + - - -
197C GLY* 3.8 2.9 - - - -
198C PRO* 4.0 1.2 - - - +
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TYR* 3.3 6.5 - - - -
44C GLY* 1.3 73.2 + - - -
46C LEU* 1.3 63.1 + - - +
47C ILE* 3.4 2.5 + - - +
52C VAL* 3.3 5.1 - - - +
53C VAL 2.8 38.3 + - - -
121C ILE* 4.1 11.0 - - - -
196C GLY 4.7 0.2 + - - -
197C GLY 4.2 1.2 - - - -
198C PRO* 3.2 34.2 - - - +
209C LEU* 3.6 27.3 - - - +
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO 5.1 0.7 - - - +
29C TYR* 2.9 17.3 + - - +
31C VAL* 4.4 9.4 - - + +
44C GLY 4.3 0.2 - - - -
45C SER* 1.3 70.7 - - - +
47C ILE* 1.4 58.0 + - - +
48C ASN 3.1 23.8 - - - +
49C SER 4.7 1.8 - - - +
51C TRP 3.7 9.6 - - - +
52C VAL* 3.9 12.6 - - + -
67C LEU* 3.7 19.3 - - + -
108C LEU* 4.4 9.2 - - + -
112C ALA* 4.8 1.3 - - + -
114C LEU* 3.8 28.0 - - + -
118C VAL* 3.9 17.3 - - + -
119C ALA 3.7 21.5 - - - +
120C SER* 3.2 1.9 - - - +
121C ILE* 2.8 30.1 + - - +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C SER 3.9 4.9 - - - +
46C LEU* 1.4 77.9 - - - +
48C ASN* 1.3 66.0 + - - +
51C TRP* 2.9 25.7 + - + +
53C VAL* 3.5 36.3 - - + +
105C LEU* 4.0 7.4 - - + -
120C SER* 3.6 10.9 - - - -
121C ILE* 3.9 19.8 - - + +
123C LEU* 4.0 23.3 - - + -
209C LEU* 4.1 11.4 - - + -
238C ILE* 3.7 26.2 - - + -
242C ILE* 4.2 10.1 - - + -
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.1 24.1 - - - +
47C ILE* 1.3 79.6 + - - +
49C SER* 1.3 64.1 + - - +
50C GLN* 2.9 17.3 + - - +
51C TRP* 3.0 36.6 + - - +
114C LEU* 5.1 1.3 - - - -
120C SER* 3.8 10.7 - - - -
242C ILE* 3.8 22.4 - - - +
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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