Contacts of the strand formed by residues 52 - 59 (chain B) in PDB entry 5IZL
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 GLY 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B THR* 5.0 1.1 - - - +
50B ASP 3.1 4.7 + - - -
51B LEU* 1.3 73.7 - - - +
53B PHE* 1.3 68.0 + - - -
54B SER 4.1 0.9 - - - -
90B LEU 3.4 1.6 - - - +
91B VAL* 3.6 2.1 - - - -
92B ASP* 2.9 45.0 + - - +
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Residues in contact with PHE 53 (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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9B ASN* 5.2 0.7 - - - -
51B LEU* 3.6 33.7 - - + -
52B GLY* 1.3 76.6 - - - -
54B SER* 1.3 63.4 + - - +
89B THR* 4.2 9.6 - - + -
90B LEU 3.4 6.7 - - - -
91B VAL* 4.1 18.2 - - + -
109B ILE* 4.2 19.5 - - + -
229B ASP* 3.0 37.0 - - + -
230B HIS* 4.3 8.5 - + + -
244B THR* 4.8 5.2 - - - -
285B ARG* 3.5 46.0 - - - +
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Residues in contact with SER 54 (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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24B ALA* 4.3 14.0 + - - +
25B ARG* 5.4 1.0 - - - -
28B SER* 3.3 23.3 + - - -
52B GLY 4.1 0.8 - - - -
53B PHE* 1.3 75.7 - - - +
55B CYS* 1.3 67.1 + - - +
89B THR* 3.5 8.3 - - - +
90B LEU* 3.1 36.4 + - - -
92B ASP* 6.0 1.6 - - - +
285B ARG* 5.5 0.3 + - - -
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Residues in contact with CYS 55 (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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5B ARG* 5.7 0.2 - - - -
28B SER* 4.0 10.7 + - - +
54B SER* 1.3 81.3 - - - +
56B PHE* 1.3 67.8 + - - +
57B SER* 6.1 0.2 - - - -
87B GLN* 2.8 52.5 - - - -
88B VAL 3.5 9.2 - - - +
89B THR* 4.4 5.6 - - + +
90B LEU 4.7 0.2 - - - +
285B ARG* 6.0 2.0 - - - +
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Residues in contact with PHE 56 (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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27B LEU* 4.0 17.5 - - + -
28B SER* 3.9 13.9 - - - +
31B ALA* 3.9 26.7 - - + -
55B CYS* 1.3 78.9 - - - +
57B SER* 1.3 67.5 + - - +
58B VAL* 4.6 7.0 - - + -
86B LEU 4.0 0.2 - - - +
87B GLN* 3.6 3.9 - - - +
88B VAL* 2.8 65.6 + - + -
90B LEU* 3.7 32.8 - - + -
206B ILE* 4.3 28.0 - - + -
209B LEU* 4.7 13.5 - - + -
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Residues in contact with SER 57 (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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5B ARG* 3.8 25.2 + - - -
31B ALA* 4.1 15.8 - - - +
56B PHE* 1.3 75.9 - - - +
58B VAL* 1.3 68.0 + - - +
85B LEU* 4.4 19.3 - - - +
86B LEU 3.2 11.0 - - - -
87B GLN* 4.5 3.1 - - - -
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Residues in contact with VAL 58 (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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31B ALA* 5.3 3.6 - - + -
56B PHE* 4.6 10.1 - - + -
57B SER* 1.3 80.5 - - - +
59B PRO* 1.3 83.0 - - + +
85B LEU* 4.2 4.0 - - - -
86B LEU* 2.7 44.8 + - + +
88B VAL* 6.0 0.9 - - + -
206B ILE* 3.8 27.4 - - + -
210B THR* 3.6 28.9 - - + +
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Residues in contact with PRO 59 (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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57B SER 5.0 0.2 - - - +
58B VAL* 1.3 99.2 - - + +
60B LEU* 1.3 66.2 + - - +
61B PRO* 3.3 8.8 - - - +
83B GLU* 6.5 0.9 - - + -
84B PRO 4.0 9.9 - - - +
85B LEU* 4.3 9.2 - - + -
210B THR* 4.6 1.4 - - - +
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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