Contacts of the helix formed by residues 140 - 148 (chain D) in PDB entry 5SY1
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 GLU 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D ASN* 3.1 20.2 + - - +
139D TYR* 1.3 88.1 - - + +
141D GLU* 1.3 59.9 + - - +
142D PHE 3.3 2.0 - - - -
143D VAL* 3.0 11.5 + - + +
144D THR* 3.0 37.1 + - + +
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Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B TRP* 5.8 0.4 - - - -
128D GLU 4.8 0.2 - - - +
129D ALA* 3.2 44.2 - - + +
131D ILE* 3.3 31.6 - - - +
132D ASP* 3.8 11.4 + - - +
137D VAL* 4.1 9.2 - - + -
138D ASN* 3.4 35.0 + - + +
139D TYR 3.5 0.8 - - - -
140D GLU* 1.3 77.5 - - - +
142D PHE* 1.3 61.7 + - - +
144D THR* 3.2 20.1 + - - -
145D MET* 3.3 22.7 - - - +
202D CA 4.2 2.7 - - - -
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Residues in contact with PHE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B TRP* 5.4 19.7 - + + -
614B TYR* 3.8 30.1 - + + -
86D ILE* 3.7 16.6 - - + -
89D ALA* 4.2 7.4 - - + -
90D PHE* 3.4 36.1 - + + -
93D PHE* 3.6 36.3 - + - -
101D ILE* 4.8 15.0 - - + -
137D VAL* 4.7 3.9 - - + +
138D ASN 4.2 4.6 + - - +
140D GLU 3.3 0.2 - - - -
141D GLU* 1.3 78.3 - - - +
143D VAL* 1.3 60.9 + - - +
145D MET* 3.6 6.5 + - - +
146D MET* 3.3 39.8 + - + +
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASP* 4.8 13.2 - - - +
86D ILE* 3.9 30.2 - - + +
90D PHE* 4.2 3.6 - - + -
139D TYR* 3.3 29.4 - - + +
140D GLU* 3.0 13.8 + - + +
142D PHE* 1.3 75.4 - - - +
144D THR* 1.3 67.7 + - + +
146D MET* 3.1 15.0 + - - +
147D THR* 3.2 23.3 + - + +
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ARG* 4.2 3.6 + - - -
131D ILE* 5.9 5.1 - - + +
140D GLU* 3.0 17.9 + - + +
141D GLU* 3.2 16.9 + - - -
143D VAL* 1.3 81.0 - - + +
145D MET* 1.3 75.2 + - - +
146D MET 3.2 0.2 - - - -
147D THR* 2.7 25.2 + - + +
148D SER* 3.4 12.0 + - - -
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ARG* 3.6 42.6 + - + +
610B TRP* 3.5 29.4 - - + -
611B GLN* 3.6 17.7 + - - -
128D GLU* 3.4 40.8 - - + +
129D ALA* 5.7 1.6 - - + -
141D GLU* 3.3 23.3 + - - +
142D PHE* 3.8 4.0 - - - +
143D VAL 3.2 0.8 - - - -
144D THR* 1.3 99.1 + - - +
146D MET* 1.3 76.1 + - + +
148D SER 4.1 1.9 - - - -
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Residues in contact with MET 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ARG 5.4 0.4 - - - +
610B TRP* 4.5 11.7 - - + -
611B GLN* 4.2 25.9 + - + +
614B TYR* 3.6 44.4 - - + -
78D LYS* 5.5 10.0 - - - +
86D ILE* 4.3 20.4 - - + -
142D PHE* 3.3 40.4 + - + +
143D VAL 3.1 8.0 + - - +
145D MET* 1.3 95.9 - - + +
147D THR* 1.3 67.9 + - + +
148D SER 4.7 0.4 - - - -
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Residues in contact with THR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ARG 5.8 0.2 - - - +
80D THR 5.0 12.3 - - - +
81D ASP* 5.8 5.8 - - + +
86D ILE* 6.1 1.1 - - + -
143D VAL* 3.3 24.5 - - + +
144D THR* 2.7 22.8 + - + +
146D MET* 1.3 81.4 - - + +
148D SER* 1.3 68.2 + - - +
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B LYS* 4.2 9.5 + - - -
607B ARG* 2.7 59.9 + - - -
611B GLN* 4.7 6.8 + - - -
75D ARG* 6.0 1.7 - - - -
144D THR 3.4 5.1 + - - -
145D MET 4.1 5.6 - - - -
147D THR* 1.3 88.1 + - - +
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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