Contacts of the strand formed by residues 180 - 191 (chain A) in PDB entry 4CAA
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 THR 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LYS* 4.2 3.8 + - - +
147A PHE* 3.5 49.0 - - + +
176A LEU* 4.2 5.9 - - + +
177A ASP* 2.5 41.5 + - - +
178A SER 3.0 3.8 - - - +
179A GLN* 1.3 80.1 - - - +
181A MET* 1.3 69.5 + - - +
182A MET 3.9 9.2 - - - +
183A VAL* 4.1 8.1 - - + -
354A LYS* 5.3 4.8 - - + +
355A ILE 3.6 15.0 - - - +
356A THR* 4.5 6.7 - - + +
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Residues in contact with MET 181 (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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120A VAL* 4.2 2.4 - - - +
121A LYS* 2.9 60.6 + - + +
124A LEU* 4.0 24.0 - - + +
147A PHE* 3.6 5.4 - - - -
179A GLN* 3.5 10.5 + - - +
180A THR* 1.3 81.9 - - - +
182A MET* 1.3 65.3 + - + +
327A LEU* 3.7 18.4 - - + -
355A ILE 3.1 9.8 + - - +
357A LEU* 3.2 56.5 - - + +
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Residues in contact with MET 182 (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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118A MET* 4.0 21.8 - - + -
119A PHE 3.3 15.0 - - - +
120A VAL* 3.8 10.5 - - + -
124A LEU* 5.5 2.2 - - + -
126A LEU* 4.3 11.0 - - + -
130A PHE* 4.6 5.8 - - + -
147A PHE* 3.7 4.3 - - - -
180A THR* 3.9 0.4 - - - +
181A MET* 1.3 82.8 - - + +
183A VAL* 1.3 68.3 + - - +
184A LEU* 3.4 38.6 - - + -
321A ILE* 4.1 28.7 - - + -
327A LEU* 4.8 6.7 - - + -
355A ILE* 2.8 51.1 + - + +
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Residues in contact with VAL 183 (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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118A MET* 3.2 3.6 - - - -
119A PHE* 3.0 32.7 + - - +
147A PHE* 4.0 19.7 - - + -
157A ILE* 4.0 23.8 - - + -
173A ILE* 4.5 6.3 - - + -
176A LEU* 4.5 10.5 - - + -
180A THR* 4.1 7.2 - - + -
182A MET* 1.3 82.4 - - - +
184A LEU* 1.3 72.9 + - - +
185A VAL* 5.1 2.7 - - + -
352A ALA* 3.9 19.3 - - + -
353A VAL 3.4 13.0 - - - +
354A LYS* 4.1 12.8 - - + +
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Residues in contact with LEU 184 (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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60A ALA* 4.8 6.0 - - + +
63A PHE* 3.6 31.9 - - + -
64A LEU* 3.9 44.6 - - + +
117A ALA 3.4 3.6 - - - +
118A MET* 3.4 27.6 - - + -
130A PHE* 4.6 6.5 - - + -
182A MET* 3.4 18.8 - - + -
183A VAL* 1.3 71.6 - - - +
185A VAL* 1.3 59.9 + - - +
321A ILE* 6.1 1.3 - - + -
352A ALA* 3.1 3.8 - - - +
353A VAL* 2.8 44.2 + - + +
355A ILE* 4.3 10.3 - - + -
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Residues in contact with VAL 185 (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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60A ALA* 5.4 2.0 - - - -
63A PHE* 4.8 3.0 - - - -
115A GLY 4.5 0.2 - - - -
116A ASN* 3.4 3.6 - - - +
117A ALA 2.8 40.8 + - - +
119A PHE* 3.3 35.7 - - + -
157A ILE* 4.9 5.2 - - + -
160A TYR* 4.2 12.7 - - + -
161A VAL* 3.8 27.1 - - + -
172A LEU* 4.4 4.7 - - + -
183A VAL* 4.8 2.2 - - + +
184A LEU* 1.3 75.6 - - - +
186A ASN* 1.3 74.6 + - - +
351A THR 3.1 14.8 - - - +
352A ALA* 4.2 7.4 - - + -
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Residues in contact with ASN 186 (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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56A SER* 2.4 45.3 + - - +
59A THR* 4.1 5.8 - - - -
60A ALA* 4.0 21.3 - - + -
63A PHE* 6.2 0.2 - - + -
114A MET* 3.4 28.2 - - - +
115A GLY 3.2 14.3 + - - -
116A ASN* 2.8 25.7 + - - +
185A VAL* 1.3 80.8 - - - +
187A TYR* 1.3 69.6 + - - +
350A ALA* 3.4 0.7 - - - -
351A THR* 2.8 26.8 + - - +
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Residues in contact with TYR 187 (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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113A SER* 4.4 17.3 + - - -
114A MET* 3.1 7.8 - - - +
115A GLY* 3.1 47.1 + - - -
160A TYR* 3.7 47.3 + + - -
161A VAL* 4.8 6.7 - - + -
164A GLY* 3.4 42.8 - - - -
165A THR* 4.1 10.1 - - + -
166A ARG* 4.9 1.9 + - - -
186A ASN* 1.3 83.0 - - - +
188A ILE* 1.3 65.2 + - - +
189A PHE 4.9 0.4 - - - -
349A ALA 3.4 7.6 - - - +
350A ALA* 3.6 17.0 - - + +
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Residues in contact with ILE 188 (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 SER* 3.6 24.0 - - - +
55A LEU* 4.7 3.6 - - + -
56A SER* 3.8 10.3 - - - -
103A LEU* 5.3 0.9 - - + -
112A LEU* 4.2 18.2 - - + -
113A SER 3.3 10.5 - - - +
114A MET* 3.9 21.1 - - + -
165A THR* 4.2 2.1 - - - +
187A TYR* 1.3 77.6 - - - +
189A PHE* 1.3 65.6 + - - +
190A PHE 4.3 0.2 - - - -
348A SER* 3.2 8.0 - - - -
349A ALA* 2.9 41.7 + - + +
383B PHE* 4.4 18.2 - - + +
384B PHE* 3.9 27.8 - - + -
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Residues in contact with PHE 189 (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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111A GLN* 3.5 29.6 - - + -
112A LEU* 3.1 6.5 - - - +
113A SER* 2.9 35.1 + - - +
164A GLY 3.6 17.0 - - - +
165A THR* 3.3 30.7 - - - -
166A ARG* 3.7 40.8 - - + +
168A LYS* 4.1 0.7 - - + -
187A TYR* 4.6 0.6 - - + -
188A ILE* 1.3 74.3 - - - +
190A PHE* 1.3 64.9 + - - +
191A LYS* 3.9 28.3 - - + -
346A GLU* 3.5 25.4 - - - -
347A ALA 4.1 1.1 - - - -
348A SER* 3.5 15.0 - - - -
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Residues in contact with PHE 190 (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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110A LEU* 3.8 13.7 - - + -
111A GLN 3.2 13.9 - - - -
112A LEU* 3.9 22.0 - - + -
189A PHE* 1.3 78.9 - - - +
191A LYS* 1.3 60.7 + - - +
192A ALA* 4.1 15.5 - - + -
244A TYR* 3.8 39.5 - + - -
248A ALA* 3.7 21.8 - - + -
346A GLU* 3.5 8.6 - - - +
347A ALA* 3.1 39.9 + - + +
374B ILE* 4.2 17.9 - - + -
383B PHE* 4.9 6.7 - + - -
384B PHE* 3.9 22.9 - + + -
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Residues in contact with LYS 191 (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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110A LEU* 3.4 1.9 - - - -
111A GLN* 2.6 67.7 + - + +
189A PHE* 3.9 19.3 - - + -
190A PHE* 1.3 76.3 - - - +
192A ALA* 1.3 61.4 + - - +
345A ARG* 3.5 30.2 + - - +
346A GLU* 3.3 27.4 + - + +
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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