Contacts of the helix formed by residues 342 - 350 (chain A) in PDB entry 5I75
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 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLU* 3.2 16.7 + - - -
147A CYS* 3.4 29.1 - - - -
165A ILE* 4.4 0.9 - - - +
340A GLY 3.7 0.6 - - - -
341A PHE* 1.3 78.3 - - - +
343A VAL* 1.3 59.0 + - - +
344A LEU 3.4 1.8 - - - +
345A LEU* 3.4 10.4 - - - +
346A ALA* 2.9 25.6 + - - +
445A GLY* 4.0 2.3 - - - -
508A GLU* 5.2 0.4 + - - -
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Residues in contact with VAL 343 (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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95A TYR* 3.5 38.4 - - + +
341A PHE* 3.3 24.8 - - + +
342A GLY* 1.3 75.1 - - - +
344A LEU* 1.3 63.6 + - + +
346A ALA* 3.2 2.6 + - - +
347A PHE* 2.9 38.1 + - + +
441A ALA* 3.5 47.8 - - + +
442A GLY* 4.0 6.3 - - - +
445A GLY* 4.4 9.2 - - - +
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Residues in contact with LEU 344 (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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92A VAL* 3.5 29.8 - - + -
95A TYR* 3.8 22.9 - - + -
133A PHE* 3.6 41.3 - - + +
136A GLU* 3.7 28.0 + - + -
137A LEU* 3.6 17.0 - - + +
338A GLY 4.2 8.3 - - - +
339A PRO* 4.0 15.7 - - + -
342A GLY 3.4 0.6 - - - +
343A VAL* 1.3 77.0 - - + +
345A LEU* 1.3 57.4 + - - +
347A PHE* 4.4 4.0 - - + -
348A ALA* 2.9 32.9 + - - +
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Residues in contact with LEU 345 (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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136A GLU* 3.6 31.3 + - - +
139A LEU* 3.8 8.1 - - + -
140A GLY* 3.3 37.8 - - - +
145A ASN 4.0 4.7 - - - +
146A GLY 3.3 32.1 - - - +
147A CYS* 3.8 8.7 - - - -
150A ILE* 3.7 29.8 - - + -
342A GLY* 3.4 12.6 + - - +
343A VAL 3.1 0.2 - - - -
344A LEU* 1.3 78.2 - - - +
346A ALA* 1.3 57.0 + - - +
349A SER* 2.9 26.8 + - - -
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Residues in contact with ALA 346 (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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145A ASN 5.1 2.5 - - - -
146A GLY* 5.8 0.9 - - - -
147A CYS* 5.3 2.0 - - - -
342A GLY 2.9 17.4 + - - +
343A VAL 3.8 2.2 - - - +
345A LEU* 1.3 73.3 - - - +
347A PHE* 1.3 71.1 + - + +
349A SER* 3.2 11.6 + - - -
350A TYR* 3.1 26.1 - - + -
444A GLU* 4.4 2.0 - - + +
445A GLY* 3.7 16.2 - - - +
448A THR* 3.7 33.2 - - + +
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Residues in contact with PHE 347 (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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88A PHE* 3.4 49.3 - + + +
91A SER* 3.0 39.9 - - - -
92A VAL* 3.9 27.1 - - + -
95A TYR* 4.4 0.2 - - + -
137A LEU* 5.5 2.5 - - + -
274A VAL* 5.8 0.9 - - + -
277A SER* 5.0 5.6 - - - -
343A VAL* 2.9 25.7 + - + +
344A LEU* 4.0 5.6 - - - +
346A ALA* 1.3 79.2 - - + +
348A ALA* 1.3 60.6 + - - +
350A TYR* 3.6 3.3 - + - +
351A ASN* 4.7 1.4 - - - +
440A PHE* 5.3 1.6 - - + -
441A ALA* 3.4 37.7 - - + -
444A GLU* 3.7 28.7 - - + -
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Residues in contact with ALA 348 (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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137A LEU* 3.1 36.3 - - + +
140A GLY* 3.7 3.1 - - - -
141A GLN* 3.2 45.5 - - + +
344A LEU 2.9 18.8 + - - +
345A LEU 3.8 0.2 - - - +
347A PHE* 1.3 74.6 - - - +
349A SER* 1.3 66.4 + - - +
350A TYR 3.3 0.4 + - - -
351A ASN* 3.4 8.5 - - - +
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Residues in contact with SER 349 (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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80A GLU 5.3 0.5 - - - +
140A GLY 3.1 15.5 + - - -
144A ARG* 3.1 52.0 + - - +
145A ASN* 4.3 6.6 + - - -
345A LEU 2.9 14.3 + - - -
346A ALA* 3.2 15.7 + - - -
348A ALA* 1.3 76.7 - - - +
350A TYR* 1.3 68.6 + - - +
351A ASN 3.1 6.2 + - - -
448A THR* 5.3 1.5 - - - +
452A ASP* 4.8 3.6 + - - -
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Residues in contact with TYR 350 (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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79A ARG* 4.6 9.2 - - + -
80A GLU* 3.2 47.8 - - + +
81A THR* 4.1 7.6 - - - +
82A TRP* 4.0 8.1 - - - +
88A PHE* 3.1 37.1 - + + -
274A VAL* 3.8 28.0 - - + -
346A ALA 3.1 26.6 + - - -
347A PHE* 3.6 2.0 + + - +
348A ALA 3.3 0.6 - - - -
349A SER* 1.3 79.1 - - - +
351A ASN* 1.3 64.4 + - - +
444A GLU* 6.1 0.4 - - + -
448A THR* 3.4 39.7 + - + +
451A LEU* 6.2 0.2 - - - +
452A ASP* 4.4 8.1 + - - -
462A ARG* 4.4 12.5 + - - -
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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