Contacts of the helix formed by residues 98 - 107 (chain C) in PDB entry 5A31
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 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C TYR* 2.8 60.6 + - + +
96C VAL* 4.1 4.8 - - + +
97C LYS* 1.3 70.7 - - - +
99C TYR* 1.3 65.2 + - - +
100C ASP* 3.3 3.1 - - + +
101C ARG* 2.8 38.9 + - + +
102C ALA* 3.3 13.9 + - - +
128C LYS* 5.2 3.8 - - - +
53P LYS* 5.2 1.3 + - - -
295P TYR 5.0 1.4 - - - +
297P ILE* 4.0 2.1 - - - +
326P ILE* 6.1 0.6 - - + +
327P ASP* 4.0 16.5 - - - +
330P ARG* 2.7 38.9 + - - +
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Residues in contact with TYR 99 (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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94C PHE* 3.5 53.4 - + - -
97C LYS* 3.3 38.7 + - + +
98C GLU* 1.3 71.7 - - - +
100C ASP* 1.3 69.0 + - - +
102C ALA* 3.2 7.7 + - - +
103C ALA* 3.0 24.4 + - - +
121C SER* 3.6 22.0 - - - +
124C LEU* 3.8 38.0 - - + +
125C SER* 4.0 8.1 - - - +
128C LYS* 3.9 25.6 - - + -
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Residues in contact with ASP 100 (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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98C GLU* 3.3 2.6 - - + -
99C TYR* 1.3 77.2 + - - +
101C ARG* 1.3 63.4 + - - +
103C ALA* 3.2 10.0 + - - +
104C HIS* 3.2 19.8 + - - +
125C SER* 3.4 24.3 + - - +
128C LYS* 6.0 2.3 - - - +
129C LYS* 4.0 18.7 + - - +
295P TYR* 4.4 31.9 - - + -
325P GLU 5.3 0.7 - - - +
326P ILE* 4.5 25.5 - - + +
327P ASP* 5.0 4.3 - - - +
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Residues in contact with ARG 101 (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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93C TYR* 2.4 36.4 + - + -
98C GLU* 2.8 53.1 + - + +
99C TYR 3.2 0.2 - - - -
100C ASP* 1.3 80.9 - - - +
102C ALA* 1.3 61.4 + - - +
104C HIS* 3.2 13.1 + - + +
105C PHE* 3.4 28.3 + - + -
53P LYS* 4.8 2.8 - - - +
263P SER* 6.0 0.2 - - - -
293P ASP* 3.5 28.8 + - - +
295P TYR* 4.1 26.8 + - + -
296P ARG* 3.4 43.1 - - - +
297P ILE* 3.6 9.5 - - - +
298P GLU* 4.6 9.5 + - - +
330P ARG* 5.6 0.8 - - - +
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Residues in contact with ALA 102 (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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90C ALA* 3.3 34.8 - - + +
93C TYR* 4.1 6.1 - - + +
94C PHE* 3.8 21.5 - - + +
98C GLU 3.3 6.5 + - - +
99C TYR* 3.2 9.1 + - - +
101C ARG* 1.3 75.1 - - - +
103C ALA* 1.3 66.6 + - - +
105C PHE* 3.2 10.8 + - - -
106C LEU* 3.3 20.2 + - - +
117C LEU* 4.9 2.0 - - + -
121C SER* 4.5 7.2 - - - -
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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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99C TYR 3.0 9.7 + - - +
100C ASP* 3.3 13.2 - - - +
102C ALA* 1.3 76.1 - - - +
104C HIS* 1.3 62.3 + - - +
106C LEU* 3.3 11.0 + - - -
107C HIS* 3.3 9.0 + - - -
118C TYR* 3.4 29.3 - - + +
121C SER* 3.3 21.7 + - - +
122C ARG* 4.5 12.3 - - + +
125C SER* 6.0 0.2 - - - +
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Residues in contact with HIS 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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100C ASP 3.2 9.5 + - - +
101C ARG* 3.6 9.0 - - + +
102C ALA 3.2 0.6 - - - -
103C ALA* 1.3 80.0 - - - +
105C PHE* 1.3 94.3 + + - +
107C HIS* 3.4 21.4 + - - +
292P GLN 5.1 4.9 + - - -
293P ASP* 5.2 1.7 + - - -
294P PRO* 3.9 34.1 - - + +
295P TYR* 4.3 17.8 - + + -
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Residues in contact with PHE 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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86C ALA* 4.2 22.1 - - - +
89C LEU* 3.8 32.5 - - + -
90C ALA* 4.2 11.9 - - + -
93C TYR* 3.5 31.6 - + - -
101C ARG* 3.4 27.8 + - + -
102C ALA* 3.2 8.2 + - - +
104C HIS* 1.3 98.9 - + - +
106C LEU* 1.3 62.3 + - - +
107C HIS 3.3 1.4 + - - -
108C GLY 4.3 4.0 + - - -
109C CYS 5.1 1.0 + - - -
57P GLU* 4.8 3.4 - - - -
60P PHE* 4.2 24.4 - + + -
293P ASP* 4.6 17.7 - - - -
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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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86C ALA* 4.5 2.0 - - + +
87C TYR* 4.0 21.3 - - + +
90C ALA* 3.6 22.9 - - + -
102C ALA 3.3 15.5 + - - +
103C ALA 3.3 2.8 + - - +
105C PHE* 1.3 76.5 - - - +
107C HIS* 1.3 62.9 + - - +
108C GLY 3.2 2.2 - - - -
109C CYS* 3.1 25.6 + - + +
114C ALA* 3.9 27.3 - - + +
115C TYR* 6.1 0.2 - - - -
117C LEU* 3.6 26.0 - - + -
118C TYR* 3.6 45.9 - - + +
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Residues in contact with HIS 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 3.3 7.9 + - - +
104C HIS* 3.4 18.8 - - - +
105C PHE 3.2 2.2 - - - -
106C LEU* 1.3 76.5 - - - +
108C GLY* 1.3 60.6 + - - +
109C CYS 3.7 2.4 + - - +
118C TYR* 3.4 39.0 + + - -
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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