Contacts of the strand formed by residues 145 - 151 (chain C) in PDB entry 3RMD
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 ARG 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C TYR* 3.1 5.1 - - - -
140C ASP 3.1 26.6 + - - -
143C ASP* 2.8 28.7 + - + +
144C ASP* 1.3 87.8 + - - +
146C PHE* 1.3 64.7 + - - +
147C TYR* 3.3 27.1 + - + +
184C ASP 5.4 2.4 + - - -
185C LYS* 3.5 31.0 - - - +
187C ILE* 3.4 25.9 - - + +
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Residues in contact with PHE 146 (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 THR* 4.3 13.7 - - + -
138C HIS 3.8 3.6 - - - -
139C TYR* 3.5 25.4 - + + +
144C ASP* 5.3 0.4 - - - -
145C ARG* 1.3 72.9 - - - +
147C TYR* 1.3 60.9 + - - +
148C VAL* 3.8 2.8 + - + +
182C ILE* 3.7 32.1 - - + -
185C LYS* 2.9 28.5 + - + +
186C ILE* 3.7 9.0 - - + -
187C ILE* 3.0 27.9 + - - +
325C ILE* 4.4 6.3 - - + -
328C VAL* 4.0 12.8 - - + -
329C TYR* 3.9 35.9 - + + -
332C LEU* 3.4 34.1 - - + -
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Residues in contact with TYR 147 (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 THR* 3.3 2.3 - - - -
138C HIS 2.8 46.1 + - - +
140C ASP* 4.5 5.4 - - + -
143C ASP* 2.8 34.4 + - + +
145C ARG* 3.3 35.6 + - + +
146C PHE* 1.3 74.5 - - - +
148C VAL* 1.3 61.5 + - - +
149C PHE* 3.3 25.4 - + + -
187C ILE* 3.9 35.7 - - + +
189C MET* 5.5 4.3 - - - -
204C PHE* 3.2 37.7 - + + -
208C LYS* 3.8 2.7 + - - -
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Residues in contact with VAL 148 (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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135C ALA* 6.3 0.4 - - + -
136C ILE 3.3 8.7 - - - +
137C THR* 4.2 13.5 - - + +
146C PHE* 4.2 4.9 - - + +
147C TYR* 1.3 74.4 - - - +
149C PHE* 1.3 73.7 + - - +
150C ASP* 4.0 1.3 - - + -
186C ILE* 3.7 29.8 - - + -
187C ILE 3.0 9.2 + - - +
188C TYR* 4.3 16.4 - - + -
189C MET* 3.0 30.9 + - - +
321C ILE* 4.2 26.5 - - + -
324C ASN* 5.6 0.4 - - - +
325C ILE* 3.9 17.0 - - + -
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Residues in contact with PHE 149 (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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135C ALA* 3.4 6.2 - - - +
136C ILE* 2.7 51.7 + - + -
138C HIS* 4.9 0.4 - - + -
147C TYR* 3.3 38.4 - + + -
148C VAL* 1.3 83.7 - - - +
150C ASP* 1.3 59.2 + - - +
189C MET* 3.4 21.1 - - - -
191C PHE* 4.6 6.7 - + - -
197C LEU* 3.1 32.5 - - + +
200C GLU* 4.5 4.7 - - - -
201C TYR* 3.5 40.4 - + + -
204C PHE* 3.5 32.3 - + + -
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Residues in contact with ASP 150 (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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134C ASP 3.6 3.7 - - - +
135C ALA* 4.8 0.7 - - - +
148C VAL* 4.0 1.9 - - + -
149C PHE* 1.3 72.5 - - - +
151C LEU* 1.3 81.0 + - - +
152C LEU* 3.3 18.7 - - - +
188C TYR* 2.7 40.0 + - + +
189C MET 3.0 8.5 + - - -
190C PRO* 3.3 4.0 - - + +
191C PHE* 2.6 34.3 + - - +
197C LEU* 3.8 3.1 - - - -
317C HIS* 3.1 28.5 + - - -
321C ILE* 3.6 15.7 - - + +
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Residues in contact with LEU 151 (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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132C PRO* 4.4 5.8 - - + -
133C ILE 4.2 8.1 - - - +
134C ASP* 3.4 35.8 + - + -
150C ASP* 1.3 82.7 + - - +
152C LEU* 1.3 59.0 + - - +
153C ASN 3.1 24.7 - - - +
154C SER* 3.5 26.2 - - - -
191C PHE* 3.9 3.4 - - + +
193C ASN* 3.6 11.0 - - - +
194C GLU* 3.5 39.7 - - + +
197C LEU* 3.8 8.2 - - + +
313C ARG* 2.7 29.0 + - - +
317C HIS* 3.7 0.7 + - - -
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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