Contacts of the strand formed by residues 164 - 175 (chain A) in PDB entry 1RI4
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 LEU 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU* 3.8 5.6 - - - +
134A PHE 3.5 15.9 - - - +
135A ASP 4.1 1.1 - - - +
137A ILE* 3.9 12.3 - - + -
160A ILE* 3.2 16.1 + - + +
161A ALA 3.5 5.4 + - - +
162A ARG 3.5 0.6 - - - -
163A HIS* 1.3 80.0 - - - +
165A ARG* 1.3 67.9 - - - +
168A GLY* 3.6 12.8 - - - +
169A TYR 3.6 38.1 - - - +
170A PHE* 4.5 4.0 - - + -
242A LEU* 3.9 25.4 - - + -
291A LYS* 2.8 51.6 + - + +
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Residues in contact with ARG 165 (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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67A SER* 5.7 3.9 - - - -
133A GLU* 3.4 40.9 + - + +
134A PHE* 3.1 18.6 + - - +
135A ASP* 3.0 43.3 + - - +
164A LEU* 1.3 76.5 - - - +
166A PRO* 1.3 68.9 - - + +
167A GLY 3.2 0.3 + - - -
168A GLY* 2.7 28.8 + - - +
291A LYS* 3.6 4.3 - - - +
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Residues in contact with PRO 166 (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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133A GLU* 4.2 14.8 - - - +
164A LEU 3.7 2.0 - - - +
165A ARG* 1.3 89.8 - - + +
167A GLY* 1.3 60.4 + - - +
168A GLY 3.4 0.2 + - - -
291A LYS* 4.1 18.8 - - + +
292A LEU 5.4 5.2 - - - +
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Residues in contact with GLY 167 (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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165A ARG 3.2 0.4 + - - -
166A PRO* 1.3 72.7 - - - +
168A GLY* 1.3 63.7 + - - +
169A TYR* 4.1 5.5 - - - -
290A ARG* 3.3 31.8 + - - -
291A LYS 2.6 24.6 + - - -
292A LEU* 5.0 1.6 + - - -
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Residues in contact with GLY 168 (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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135A ASP* 3.3 16.6 - - - -
164A LEU* 3.6 11.1 - - - +
165A ARG* 2.7 21.0 + - - -
166A PRO 3.2 1.0 + - - -
167A GLY* 1.3 81.8 - - - +
169A TYR* 1.3 61.7 + - - -
290A ARG* 3.3 4.5 - - - +
291A LYS* 3.0 24.5 + - - +
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Residues in contact with TYR 169 (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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61A TYR* 3.4 56.5 - + + -
135A ASP 3.1 11.3 + - - +
136A VAL* 3.3 13.1 - - + +
137A ILE 2.9 25.6 + - - -
164A LEU* 3.6 6.7 - - - +
167A GLY 4.1 3.8 - - - -
168A GLY* 1.3 77.2 - - - -
170A PHE* 1.3 59.9 + - - +
171A ILE* 4.0 3.6 - - + -
245A VAL* 4.3 10.5 - - + +
288A VAL* 3.7 12.6 - - + -
289A PHE 3.5 4.9 - - - -
290A ARG* 3.5 52.9 + - + -
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Residues in contact with PHE 170 (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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71A LEU* 4.9 1.1 - - + -
137A ILE* 3.3 31.2 - - + -
139A SER* 4.1 15.0 - - - -
143A PHE* 4.2 19.3 - + - -
160A ILE* 3.3 32.5 - - + -
164A LEU* 4.5 3.4 - - + -
169A TYR* 1.3 74.6 - - - +
171A ILE* 1.3 68.5 + - - +
172A MET* 3.6 26.5 - - + -
237A PHE* 3.6 34.3 - + - -
242A LEU* 4.3 10.3 - - + -
287A VAL 3.8 0.7 - - - +
288A VAL* 3.4 4.9 - - - -
289A PHE* 2.7 45.8 + + + +
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Residues in contact with ILE 171 (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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57A LEU* 4.1 18.8 - - + +
58A ILE* 4.4 24.9 - - + -
61A TYR* 4.2 28.0 - - + -
62A THR* 5.4 2.7 - - + -
82A TYR* 4.4 0.9 - - - +
136A VAL* 4.2 16.6 - - + -
137A ILE 2.9 5.5 + - - +
138A SER* 3.4 32.7 - - - +
139A SER 2.9 23.4 + - - -
140A GLN* 3.9 5.6 - - - +
169A TYR* 4.8 0.9 - - + -
170A PHE* 1.3 82.5 - - - +
172A MET* 1.3 62.5 + - - +
287A VAL 3.9 3.8 - - - -
288A VAL* 4.0 19.3 - - + -
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Residues in contact with MET 172 (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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57A LEU* 4.4 0.6 - - - +
139A SER* 3.1 22.9 - - - +
140A GLN* 4.0 3.1 + - - -
143A PHE* 3.8 18.8 - - + -
170A PHE* 3.6 27.4 - - + -
171A ILE* 1.3 77.4 - - - +
173A THR* 1.3 70.4 + - - +
174A VAL* 3.8 21.5 - - + -
233A MET* 3.7 15.7 - - + +
286A VAL* 3.7 4.2 - - - +
287A VAL* 3.1 51.6 + - + +
289A PHE* 3.5 33.9 - - + -
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Residues in contact with THR 173 (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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53A ILE* 4.9 4.9 - - + -
54A LYS* 5.3 0.7 - - + -
57A LEU* 4.0 12.3 - - + -
139A SER 3.3 3.4 + - - -
140A GLN* 2.7 44.8 + - - +
141A PHE* 2.8 46.6 + - + -
172A MET* 1.3 79.2 - - - +
174A VAL* 1.3 62.2 + - - +
250A PHE* 3.7 35.4 - - + -
284A TYR* 4.9 1.1 - - - -
285A GLU 3.4 6.3 - - - +
286A VAL* 4.6 4.0 - - + -
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Residues in contact with VAL 174 (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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139A SER 5.2 0.2 - - - +
143A PHE* 3.8 31.2 - - + +
144A HIS* 4.0 15.0 - - + +
172A MET* 3.8 24.5 - - + -
173A THR* 1.3 78.9 - - - +
175A PRO* 1.3 82.3 - - + +
228A VAL* 4.1 20.0 - - + -
230A PHE* 6.1 0.4 - - + -
233A MET* 5.9 0.2 - - + -
284A TYR* 3.9 5.4 - - - -
285A GLU* 3.0 28.0 + - + +
287A VAL* 4.3 15.0 - - + -
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Residues in contact with PRO 175 (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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144A HIS* 3.7 35.0 - - + +
174A VAL* 1.3 100.2 - - + +
176A SER* 1.3 60.3 + - - +
177A ARG 3.8 2.5 + - - -
180A ILE* 4.2 9.6 - - + -
212A TYR* 3.5 25.4 - - - +
225A GLU* 4.7 2.2 - - - +
226A TYR 6.1 0.7 - - - +
227A PHE* 6.4 0.4 - - + -
228A VAL* 4.1 12.7 + - + +
283A ILE* 3.6 14.6 - - + +
284A TYR* 3.5 25.8 - - + -
285A GLU* 4.2 2.3 - - - +
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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