Contacts of the strand formed by residues 30 - 33 (chain L) in PDB entry 5G04
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 30 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1291A ARG* 5.2 2.2 - - - +
1352A ILE* 5.2 7.6 - - + -
1353A LYS 3.5 15.9 - - - +
1354A GLU* 3.8 17.3 - - + -
1355A GLY 4.4 2.5 - - - +
1358A ILE 5.8 0.2 - - - -
1359A ASN* 3.5 47.1 - - + +
1361A ASP* 5.0 0.7 - - - +
28L GLN 4.1 3.1 + - - +
29L ALA* 1.3 73.1 - - - +
31L TRP* 1.3 58.9 + - - +
32L SER* 4.0 2.7 + - - +
65L ASN 3.2 14.2 - - - +
66L ILE* 3.3 3.1 - - - -
67L GLN* 3.0 49.5 + - + +
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Residues in contact with TRP 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351A GLN 3.4 5.5 - - - +
1352A ILE* 3.5 0.9 - - - +
1353A LYS* 3.1 40.8 + - + +
26L GLY* 3.4 26.7 + - - -
29L ALA* 3.1 27.8 + - + +
30L VAL* 1.3 72.5 - - - +
32L SER* 1.3 59.2 + - - +
33L LEU* 5.5 1.6 - - + -
42L VAL* 3.6 23.0 - - + +
45L LEU* 4.2 16.6 - - + -
46L ARG* 3.2 40.1 - - + +
64L VAL* 3.6 32.5 - - + -
65L ASN 3.7 2.2 - - - -
66L ILE* 3.6 34.1 - - + +
156L ILE* 3.7 24.2 - - + -
158L ILE* 4.5 9.0 - - + -
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Residues in contact with SER 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351A GLN 3.3 3.1 - - - -
1352A ILE* 3.6 31.9 - - - +
30L VAL* 4.4 1.7 + - - +
31L TRP* 1.3 72.6 - - - +
33L LEU* 1.3 63.9 + - - +
34L SER 3.9 0.4 - - - -
64L VAL* 3.4 6.5 - - - -
65L ASN* 2.9 57.0 + - - +
67L GLN* 4.0 8.5 + - - -
102L PHE* 4.6 5.5 - - - -
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Residues in contact with LEU 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288A CYS 5.5 0.3 - - - +
1350A TYR 4.6 2.2 - - - +
1351A GLN* 2.7 34.0 + - - +
1352A ILE* 5.2 2.1 - - - +
31L TRP* 5.6 1.8 - - + -
32L SER* 1.3 83.0 - - - +
34L SER* 1.3 63.9 + - - +
35L SER 3.3 14.9 + - - +
42L VAL* 3.4 39.3 - - + +
45L LEU* 4.3 7.9 - - + -
54L TRP* 3.4 59.0 - - + -
63L LEU 3.5 5.6 - - - +
64L VAL* 3.8 17.9 - - + -
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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