Contacts of the strand formed by residues 30 - 35 (chain B) in PDB entry 3ULA
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 ALA 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN* 4.9 0.2 - - - -
27B SER* 2.5 51.7 + - - +
28B SER 3.6 0.2 - - - -
29B ASP* 1.3 81.7 - - - +
31B SER* 1.3 57.4 + - - +
32B ILE* 5.5 0.7 - - - -
51B CYS* 5.3 0.4 - - - -
52B ILE 5.0 3.8 - - - +
54B LEU* 4.0 18.4 - - + -
153B ILE* 4.0 14.1 - - + -
154B LEU 3.0 20.0 - - - +
155B HIS* 4.5 2.2 - - - +
156B GLN* 5.1 4.9 + - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 5.0 3.8 - - - -
25B CYS 3.3 5.8 - - - -
26B ASN* 3.1 32.5 + - - -
30B ALA* 1.3 76.4 - - - +
32B ILE* 1.3 66.2 + - - +
152B VAL 3.8 1.0 - - - +
153B ILE* 3.3 24.5 - - - +
154B LEU* 3.3 20.2 + - - +
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.9 6.9 - - - -
24B VAL* 2.9 44.4 + - + +
25B CYS* 2.8 35.5 + - - +
30B ALA* 5.5 0.7 - - + -
31B SER* 1.3 79.2 - - - +
33B SER* 1.3 68.8 + - - +
48B VAL* 4.7 7.6 - - + -
51B CYS* 4.1 2.2 - - - -
52B ILE* 3.5 35.9 - - + +
151B PHE* 4.2 20.4 - - + -
152B VAL 3.8 4.9 - - - +
153B ILE* 3.8 20.0 - - + -
401C E55 4.8 9.4 - - + -
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN* 4.2 17.2 + - - +
22B TYR 3.0 25.4 - - - -
23B TRP* 4.1 3.6 - - - -
24B VAL* 3.9 5.8 - - - -
32B ILE* 1.3 81.4 - - - +
34B TYR* 1.3 62.8 + - - +
151B PHE* 3.3 6.5 - - - +
152B VAL* 2.8 44.5 + - - +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN* 3.8 2.1 - - - +
22B TYR* 3.2 51.6 + + + +
23B TRP 5.8 0.2 - - - -
24B VAL* 3.5 26.9 - - + -
33B SER* 1.3 76.6 - - - +
35B THR* 1.3 74.0 + - - +
36B TYR* 3.8 26.4 + + - -
44B ILE* 2.9 30.9 + - + +
46B ILE* 4.1 20.6 + - + +
149B LEU* 3.7 22.0 - - + -
150B GLU 2.8 15.3 - - - +
151B PHE* 3.8 26.2 - + + -
152B VAL* 6.0 0.7 - - - -
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 4.0 29.8 - - - +
20B LYS 4.3 7.0 - - - +
21B GLN* 3.7 22.2 - - - +
22B TYR* 4.8 0.4 - - - -
34B TYR* 1.3 89.4 + - - +
36B TYR* 1.3 79.8 + - - +
149B LEU* 4.7 0.7 - - - -
150B GLU* 3.0 39.7 + - - +
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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
------------------------------------------------------------
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