Contacts of the helix formed by residues 121 - 129 (chain A) 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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ASN* 2.7 27.4 + - - +
120A LYS* 1.3 76.8 + - - +
122A PHE* 1.3 61.2 + - - +
124A MET* 3.3 33.3 + - + +
125A ILE* 3.6 14.8 - - - +
450B ASN* 4.4 23.9 - - - +
451B LEU* 5.5 1.3 - - - -
452B TRP* 4.9 7.1 + - - -
453B PRO* 4.5 22.4 - - + +
454B PHE* 5.2 7.5 - - + +
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Residues in contact with PHE 122 (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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117A VAL 4.6 4.5 - - - -
118A ALA* 3.3 23.6 - - + +
119A ASN* 2.5 22.7 + - + +
121A GLU* 1.3 74.7 - - - +
123A TRP* 1.3 59.4 + - - +
125A ILE* 3.3 34.4 + - + +
126A LEU* 4.1 28.0 + - + +
453B PRO* 4.0 27.1 - - + -
457B THR* 5.4 7.0 - - + -
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Residues in contact with TRP 123 (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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111A LEU* 4.4 21.2 - - - +
112A PRO* 6.0 0.4 - - + -
116A GLU 4.6 4.3 - - - +
117A VAL* 3.5 31.9 + - + +
120A LYS* 2.9 14.6 + - + +
122A PHE* 1.3 77.6 - - - +
124A MET* 1.3 57.0 + - + +
125A ILE 3.2 6.3 + - - -
126A LEU* 4.5 8.1 + - - +
127A ALA* 4.7 8.0 + - - +
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Residues in contact with MET 124 (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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104A MET* 4.6 16.0 - - + +
107A SER 5.7 0.2 - - - +
108A HIS* 3.2 30.7 - - + +
109A HIS 5.7 2.0 - - - +
110A PRO* 5.2 7.4 - - + -
120A LYS* 3.3 11.5 + - + +
121A GLU* 3.7 33.2 - - + +
122A PHE 3.2 1.8 - - - -
123A TRP* 1.3 77.7 - - + +
125A ILE* 1.3 62.4 + - - +
127A ALA* 4.8 7.9 - - - -
128A LEU* 4.9 3.1 - - - +
454B PHE* 5.0 7.9 - - + -
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Residues in contact with ILE 125 (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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121A GLU 3.6 17.5 - - - +
122A PHE* 3.3 28.0 - - + +
123A TRP 3.2 1.4 - - - -
124A MET* 1.3 81.8 - - - +
126A LEU* 1.3 68.6 + - + +
127A ALA 3.1 4.5 - - - -
128A LEU* 3.0 38.0 + - + +
129A LEU* 4.1 1.6 + - + +
453B PRO 3.8 11.4 - - - +
454B PHE* 3.7 41.3 - - + +
457B THR* 3.6 30.3 - - + +
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Residues in contact with LEU 126 (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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122A PHE* 4.1 27.2 + - + +
123A TRP* 4.5 5.3 + - - +
125A ILE* 1.3 85.3 - - + +
127A ALA* 1.3 57.0 + - - +
128A LEU 3.1 0.2 - - - -
129A LEU* 2.9 44.3 + - + +
130A TYR* 3.1 12.9 + - - +
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Residues in contact with ALA 127 (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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104A MET* 3.6 28.4 - - + +
111A LEU* 3.7 26.2 - - + -
123A TRP 4.7 9.9 + - - +
124A MET* 5.1 3.1 - - - -
125A ILE 3.1 2.7 - - - +
126A LEU* 1.3 74.9 - - - +
128A LEU* 1.3 64.0 + - - +
130A TYR* 3.3 16.4 + - + -
131A TYR* 3.5 22.7 + - + +
498B LEU* 4.9 1.4 - - - +
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Residues in contact with LEU 128 (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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101A LEU* 3.8 20.4 - - + -
104A MET* 3.8 24.7 - - + -
124A MET 4.9 2.5 - - - +
125A ILE* 3.0 27.0 + - + +
127A ALA* 1.3 77.7 - - - +
129A LEU* 1.3 59.7 + - + +
130A TYR 3.3 0.2 - - - -
132A PRO* 3.4 20.3 - - - +
454B PHE* 5.3 9.0 - - + -
457B THR* 5.7 2.9 - - - +
458B LEU* 6.3 0.9 - - + -
495B ILE 4.6 2.3 - - - +
498B LEU* 3.8 30.9 - - + +
499B VAL* 4.1 24.0 - - + +
502B MET* 4.5 20.2 - - + -
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Residues in contact with LEU 129 (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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125A ILE* 5.2 0.9 - - + +
126A LEU* 2.9 33.3 + - + +
128A LEU* 1.3 76.5 - - + +
130A TYR* 1.3 57.9 + - - +
132A PRO* 4.1 4.7 - - - +
133A THR* 2.7 23.6 + - - -
495B ILE* 3.9 37.1 - - + +
496B LEU* 4.6 8.3 - - + -
499B VAL* 4.2 19.1 - - + -
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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