Contacts of the strand formed by residues 33 - 37 (chain A) in PDB entry 2YRZ
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 SER 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.3 6.4 - - - -
29A LEU* 3.2 18.6 - - - +
30A GLY* 2.7 44.4 + - - +
31A PRO* 3.5 0.9 - - - +
32A THR* 1.3 82.1 + - - +
34A LEU* 1.3 72.1 + - - +
77A VAL 3.3 6.3 - - - -
78A GLU* 3.5 24.0 - - - -
80A LEU* 4.6 0.6 - - - +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.8 26.9 - - + -
28A ALA* 3.4 32.1 - - + +
29A LEU* 3.4 7.4 - - - -
33A SER* 1.3 80.3 - - - +
35A ARG* 1.3 58.3 + - - +
36A VAL* 5.7 0.7 - - + -
76A VAL* 3.1 12.3 - - - +
77A VAL* 2.6 46.0 + - + +
80A LEU* 3.4 25.1 - - + -
86A TYR* 5.9 0.4 - - + -
88A PHE* 4.3 8.1 - - + -
106A ILE* 3.7 25.1 - - + -
108A ILE* 3.5 21.8 - - + -
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Residues in contact with ARG 35 (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 VAL 2.5 23.9 - - - +
26A PHE* 3.2 0.8 - - - -
27A SER* 3.1 38.2 + - - +
29A LEU* 3.8 11.3 - - + +
34A LEU* 1.3 79.4 - - - +
36A VAL* 1.3 56.7 + - - +
37A SER* 3.8 4.3 + - - -
74A SER* 4.0 25.6 + - - -
75A VAL 3.3 13.5 - - - +
76A VAL* 4.0 15.5 - - + +
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Residues in contact with VAL 36 (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 LEU* 4.0 13.7 - - + -
25A VAL 3.2 2.5 - - - -
26A PHE* 3.2 37.2 - - + -
34A LEU* 4.3 1.1 - - + -
35A ARG* 1.3 73.3 - - - +
37A SER* 1.3 61.3 + - - +
38A TRP* 3.2 11.7 - - + -
52A VAL* 4.6 3.6 - - + -
74A SER* 3.2 1.0 - - - -
75A VAL* 2.8 46.4 + - + +
77A VAL* 4.9 2.6 - - + +
88A PHE* 3.7 24.5 - - + -
90A VAL* 3.5 31.9 - - + -
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Residues in contact with SER 37 (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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23A ARG 4.0 0.7 - - - +
24A LEU* 3.4 5.3 - - - -
25A VAL* 2.8 53.2 + - - +
35A ARG* 5.0 5.6 - - - -
36A VAL* 1.3 77.4 - - - +
38A TRP* 1.3 66.5 + - - +
73A THR* 3.2 14.5 + - - -
74A SER* 3.8 13.1 - - - -
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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