Contacts of the helix formed by residues 102 - 113 (chain C) 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 SER 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C PHE 3.6 2.1 + - - -
101C ILE* 1.3 79.7 - - - +
103C ALA* 1.3 59.9 + - - +
104C ALA* 3.1 10.7 + - - +
105C GLU* 2.6 44.7 + - - +
106C LEU* 2.9 25.1 + - - +
126C ILE* 5.5 3.4 - - - +
136C GLN* 3.8 14.6 + - - +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C SER* 1.3 72.4 - - - +
104C ALA* 1.3 58.7 + - - +
106C LEU* 3.4 8.8 + - - +
107C ARG* 3.1 54.4 + - - +
122C VAL* 5.3 3.8 - - + -
123C ASP* 5.1 7.9 - - - +
126C ILE* 4.8 19.7 - - + +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C SER* 3.1 8.3 + - - +
103C ALA* 1.3 76.3 - - - +
105C GLU* 1.3 64.5 + - + +
106C LEU 3.2 0.2 - - - -
107C ARG* 3.4 21.3 + - - +
108C HIS* 3.4 19.4 + - - +
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Residues in contact with GLU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL 5.4 0.2 - - - +
93C PHE 3.8 17.4 - - - +
94C ASP* 3.0 11.3 - - - +
95C LYS* 4.2 15.2 + - + +
96C ASP* 2.2 40.3 + - - +
100C PHE 2.9 10.8 - - - +
101C ILE* 3.6 7.3 - - + -
102C SER* 2.6 28.1 + - - +
104C ALA* 1.3 73.4 - - + +
106C LEU* 1.3 62.8 + - - +
108C HIS* 3.6 16.7 - - - +
109C VAL* 3.8 10.7 - - - +
201C CA 2.4 18.7 - - - -
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A TRP* 4.6 7.6 - - + +
613A LEU* 4.4 22.7 - - + -
93C PHE* 4.9 16.6 - - + -
101C ILE* 4.6 9.6 - - + +
102C SER 2.9 17.7 + - - +
103C ALA* 3.6 7.6 - - - +
104C ALA 3.2 0.4 - - - -
105C GLU* 1.3 77.0 - - - +
107C ARG* 1.3 58.1 + - - +
108C HIS 3.1 0.2 - - - -
109C VAL* 3.0 24.3 + - + +
110C MET* 3.4 14.6 + - + +
122C VAL* 3.7 27.6 - - + -
125C MET* 4.1 15.3 - - - -
126C ILE* 4.1 23.6 - - + -
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ALA* 3.1 39.7 + - - +
104C ALA* 3.4 30.7 + - - +
106C LEU* 1.3 72.3 - - - +
108C HIS* 1.3 55.6 + - - +
109C VAL 3.2 0.2 - - - -
110C MET* 3.8 14.4 - - - +
111C THR* 2.4 39.3 + - - +
115C GLU* 4.3 20.5 - - + +
119C ASP* 3.3 31.4 + - - +
122C VAL* 4.3 17.8 - - + +
123C ASP* 4.9 3.0 + - - -
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Residues in contact with HIS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL* 5.2 6.3 - - + -
95C LYS* 3.2 45.1 + - + -
104C ALA 3.4 10.9 + - - +
105C GLU* 3.6 13.9 - - - +
106C LEU 3.1 0.6 - - - -
107C ARG* 1.3 78.4 - - - +
109C VAL* 1.3 61.6 + - + +
111C THR* 3.4 11.4 - - + +
112C ASN* 2.9 53.9 + - - -
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A LEU* 5.0 9.9 - - + -
617A VAL* 4.5 10.5 - - + -
92C VAL* 4.1 25.8 - - + +
93C PHE* 4.1 35.2 - - + -
105C GLU 3.8 12.3 - - - +
106C LEU* 3.0 12.3 + - + +
108C HIS* 1.3 79.7 - - + +
110C MET* 1.3 60.6 + - + +
112C ASN* 3.0 12.6 + - + +
113C LEU* 2.9 43.4 + - + +
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Residues in contact with MET 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A LEU* 4.8 23.1 - - + -
106C LEU* 3.4 13.9 + - + +
107C ARG* 4.0 13.9 - - - +
109C VAL* 1.3 73.6 - - - +
111C THR* 1.3 57.2 + - - +
113C LEU* 4.1 5.2 - - - +
114C GLY 2.7 14.7 + - - -
115C GLU* 2.4 42.6 + - + +
116C LYS* 3.6 11.2 - - + +
117C LEU* 3.6 48.0 - - + +
122C VAL* 3.9 24.0 - - + -
125C MET* 5.0 7.9 - - + -
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Residues in contact with THR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG* 2.4 27.5 + - - +
108C HIS* 3.4 14.5 - - + +
109C VAL 3.2 0.2 - - - -
110C MET* 1.3 77.1 - - - +
112C ASN* 1.3 63.4 + - - +
113C LEU 3.5 0.2 + - - -
114C GLY* 4.0 5.0 + - - -
115C GLU* 4.1 17.8 + - - +
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Residues in contact with ASN 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A VAL* 5.3 0.3 - - - +
627A LYS* 4.1 6.1 + - - -
92C VAL* 5.8 5.3 - - - +
108C HIS* 2.9 47.7 + - - +
109C VAL* 3.0 13.7 + - + +
111C THR* 1.3 79.9 - - - +
113C LEU* 1.3 73.3 + - + +
114C GLY 3.6 0.8 + - - -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A LEU* 4.6 14.8 - - + -
616A LEU* 4.1 31.7 - - + +
617A VAL* 4.6 11.2 - - + -
623A VAL* 3.7 31.9 - - + -
626A ARG* 4.9 7.6 + - - -
627A LYS* 3.2 17.9 - - - +
109C VAL* 2.9 32.8 + - + +
110C MET* 3.1 7.3 + - - -
112C ASN* 1.3 92.5 - - + +
114C GLY* 1.3 55.4 + - - +
115C GLU 3.5 2.6 + - - -
116C LYS* 5.1 3.1 + - - +
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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