Contacts of the helix formed by residues 135 - 143 (chain C) in PDB entry 1SMR
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 PRO 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA* 3.6 35.0 - - + +
99C GLN* 4.0 3.1 - - - +
122C GLY 4.7 5.8 - - - +
123C MET* 6.1 0.4 - - - -
124C GLY 4.6 5.4 - - - +
125C PHE 4.2 0.7 - - - -
126C PRO* 3.7 32.5 - - + -
129C ALA* 4.5 0.2 - - + -
133C VAL* 3.7 6.5 - - + +
134C THR* 1.4 94.2 - - + +
136C VAL* 1.3 65.8 + - - +
137C PHE* 3.4 5.4 - - + +
138C ASP* 3.1 26.2 + - + +
139C HIS* 3.1 18.5 + - - -
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Residues in contact with VAL 136 (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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37C ASN 6.2 0.2 - - - -
38C LEU* 4.1 24.2 - - + +
89C VAL* 5.0 3.6 - - + -
91C VAL* 4.1 25.6 - - + -
96C VAL* 4.2 12.7 - - + +
99C GLN* 3.4 36.4 + - + +
121C LEU* 4.2 28.3 - - + -
122C GLY 5.0 2.9 + - - +
123C MET* 5.9 0.2 - - - -
135C PRO* 1.3 71.4 - - - +
137C PHE* 1.3 59.5 + - - +
139C HIS* 3.0 20.1 + - - +
140C ILE* 3.0 17.8 + - + +
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Residues in contact with PHE 137 (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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122C GLY 5.4 1.0 + - - -
123C MET* 3.9 35.6 - - + +
124C GLY 5.8 1.6 - - - +
135C PRO* 3.4 3.4 - - + +
136C VAL* 1.3 77.7 - - - +
138C ASP* 1.3 58.4 + - - +
140C ILE* 3.1 14.9 + - + +
141C LEU* 2.8 55.7 + - + +
146C LEU* 3.7 32.3 - - + -
149C LYS 4.5 3.8 - - - -
150C VAL 3.7 19.3 - - - -
151C PHE* 3.8 22.4 - + + -
167C LEU* 4.0 21.3 - - + -
315C ARG* 4.0 21.1 - - + +
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Residues in contact with ASP 138 (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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124C GLY 4.3 1.0 - - - +
126C PRO* 3.6 25.5 - - - +
134C THR* 3.7 17.0 - - + -
135C PRO* 3.1 21.3 + - + +
137C PHE* 1.3 75.3 - - - +
139C HIS* 1.3 63.0 + - - +
141C LEU* 3.5 11.7 + - - +
142C SER* 3.2 22.7 + - - -
315C ARG* 2.8 42.2 + - - -
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Residues in contact with HIS 139 (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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96C VAL* 3.6 17.0 - - + +
97C THR 3.4 24.4 + - - -
99C GLN* 2.7 29.1 + - - -
100C THR 5.1 2.0 - - - -
134C THR* 3.6 35.1 + - + -
135C PRO 3.1 10.1 + - - -
136C VAL 3.0 8.5 + - - +
138C ASP* 1.3 76.1 - - - +
140C ILE* 1.3 67.0 + - - +
142C SER* 3.2 16.8 + - - -
143C GLN* 3.3 16.0 + - - +
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Residues in contact with ILE 140 (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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91C VAL* 4.2 25.1 - - + -
94C ILE* 3.9 23.8 - - + -
96C VAL* 3.9 15.3 - - + -
136C VAL* 3.0 20.5 + - + +
137C PHE* 3.1 18.6 + - + +
139C HIS* 1.3 77.7 - - - +
141C LEU* 1.3 61.9 + - - +
143C GLN* 3.1 19.9 + - - +
144C GLY 3.7 4.7 + - - -
145C VAL* 4.1 8.2 + - + -
146C LEU* 3.8 33.4 - - + +
167C LEU* 4.4 17.0 - - + -
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Residues in contact with LEU 141 (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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137C PHE* 2.8 52.9 + - + +
138C ASP* 3.5 13.2 - - - +
140C ILE* 1.3 76.5 - - - +
142C SER* 1.3 61.4 + - - +
144C GLY* 3.2 14.3 + - - -
146C LEU* 4.3 8.3 - - + -
149C LYS* 3.7 46.0 - - + -
315C ARG* 4.1 31.2 - - + +
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Residues in contact with SER 142 (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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138C ASP 3.2 10.2 + - - -
139C HIS* 3.4 16.8 - - - -
140C ILE 3.1 0.6 - - - -
141C LEU* 1.3 76.5 - - - +
143C GLN* 1.3 57.0 + - - +
144C GLY* 2.9 9.1 + - - -
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Residues in contact with GLN 143 (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 ILE* 3.9 20.0 - - - +
95C THR 3.5 21.9 + - - +
96C VAL* 4.1 11.8 - - - +
139C HIS* 3.4 13.3 + - - +
140C ILE* 3.1 11.8 + - - +
142C SER* 1.3 73.5 - - - +
144C GLY* 1.3 64.9 - - - +
145C VAL* 3.5 24.0 + - + +
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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