Contacts of the strand formed by residues 111 - 121 (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 GLN 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A SER* 4.4 9.6 - - - -
107A SER 5.6 1.8 - - - +
110A LEU* 1.3 73.3 - - - +
112A LEU* 1.3 64.2 + - - +
166A ARG* 3.9 22.9 - - - +
189A PHE* 3.5 23.3 - - + -
190A PHE* 3.2 6.5 - - - -
191A LYS* 2.6 69.5 + - + +
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Residues in contact with LEU 112 (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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103A LEU* 3.4 55.7 - - + +
104A ASN* 4.2 0.5 - - - -
105A GLN* 4.2 5.5 + - + -
106A SER* 3.4 26.2 + - - -
110A LEU* 4.1 11.8 + - + +
111A GLN* 1.3 77.1 - - - +
113A SER* 1.3 61.8 + - - +
166A ARG* 6.2 0.4 - - - +
188A ILE* 4.2 15.7 - - + -
189A PHE* 3.1 16.9 + - - +
190A PHE* 3.9 25.1 - - + -
247A ASN 5.8 2.9 - - - +
383B PHE* 4.1 18.6 - - + -
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.1 4.0 - - - -
104A ASN* 3.4 14.8 - - - -
106A SER* 4.7 8.5 - - - -
112A LEU* 1.3 76.7 - - - +
114A MET* 1.3 62.9 + - - +
166A ARG* 3.3 32.9 + - - -
187A TYR* 3.9 9.6 + - - +
188A ILE* 3.3 5.5 - - - +
189A PHE* 2.9 35.1 + - - +
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Residues in contact with MET 114 (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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55A LEU* 3.6 36.1 - - + -
56A SER* 4.1 12.1 - - - +
59A THR* 4.0 11.2 - - - -
99A LEU* 4.8 2.9 - - - -
100A LEU* 3.6 25.0 - - + +
103A LEU* 3.5 15.9 - - + +
104A ASN* 2.9 31.1 + - - +
113A SER* 1.3 75.5 - - - +
115A GLY* 1.3 62.8 + - - +
186A ASN* 3.4 26.2 - - - +
187A TYR* 3.1 11.2 - - - +
188A ILE* 3.9 23.8 - - + -
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Residues in contact with GLY 115 (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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100A LEU* 5.6 0.7 - - - -
114A MET* 1.3 77.1 - - - +
116A ASN* 1.3 66.9 + - - +
160A TYR* 4.3 7.2 - - - -
185A VAL 4.0 0.2 - - - +
186A ASN* 3.2 24.8 + - - -
187A TYR* 3.1 32.1 + - - -
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Residues in contact with ASN 116 (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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59A THR* 3.6 16.1 - - - +
63A PHE* 4.1 21.2 - - + -
100A LEU* 3.5 25.3 - - - +
115A GLY* 1.3 73.9 - - - -
117A ALA* 1.3 63.4 + - - +
138A TYR* 2.8 34.8 + - - +
139A GLY 3.0 22.3 + - - +
140A SER* 3.4 6.1 - - - +
141A GLU* 4.2 3.1 + - - -
160A TYR* 3.7 4.8 + - - -
185A VAL 3.4 3.7 - - - +
186A ASN* 2.8 34.2 + - - +
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Residues in contact with ALA 117 (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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63A PHE* 3.9 3.2 - - - -
116A ASN* 1.3 75.3 - - - +
118A MET* 1.3 61.9 + - - +
119A PHE* 4.5 2.2 - - + -
140A SER* 3.3 9.4 + - - -
141A GLU* 4.2 5.4 - - - +
143A PHE* 4.0 19.7 - - + -
160A TYR* 3.2 33.2 - - + +
184A LEU* 3.4 2.9 - - - -
185A VAL* 2.8 38.5 + - + +
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Residues in contact with MET 118 (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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63A PHE* 4.3 7.2 - - - -
117A ALA* 1.3 76.3 - - - +
119A PHE* 1.3 61.8 + - - +
120A VAL* 3.4 6.1 + - + -
126A LEU* 3.6 29.6 - - + -
130A PHE* 3.6 27.4 - - + -
131A THR* 4.8 10.8 - - + -
134A ALA* 4.6 6.7 - - + -
140A SER* 3.7 5.4 - - - +
141A GLU 2.8 30.0 + - - +
142A ALA* 3.4 26.9 - - + -
143A PHE* 3.2 14.9 + - - +
182A MET* 4.0 9.4 - - + -
183A VAL 3.2 7.0 - - - +
184A LEU* 3.4 24.9 - - + -
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Residues in contact with PHE 119 (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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117A ALA* 4.5 4.0 - - + -
118A MET* 1.3 69.8 - - - +
120A VAL* 1.3 60.9 + - - +
143A PHE* 3.4 40.4 - + + +
145A THR* 2.9 21.8 - - + +
147A PHE* 3.1 19.9 - - + -
156A LEU* 4.0 23.3 - - + -
157A ILE* 3.4 42.8 - - + -
160A TYR* 3.8 32.5 - + + -
182A MET* 4.3 1.6 - - - -
183A VAL 3.0 25.0 + - - +
185A VAL* 3.3 28.3 - - + -
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Residues in contact with VAL 120 (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* 3.4 4.9 + - + +
119A PHE* 1.3 73.2 - - - +
121A LYS* 1.3 79.8 + - - +
122A GLU* 3.1 0.5 + - - -
124A LEU* 3.7 25.6 - - + +
126A LEU* 4.1 29.8 - - + -
142A ALA* 4.1 26.2 - - + -
143A PHE 3.1 10.3 + - - +
144A ALA* 3.6 3.6 - - - -
145A THR 3.0 18.6 + - - -
147A PHE* 4.0 0.7 - - - -
181A MET 4.2 5.6 - - - +
182A MET* 3.8 14.6 - - + -
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Residues in contact with LYS 121 (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* 1.3 77.5 - - - +
122A GLU* 1.3 70.0 + - - +
123A GLN* 2.8 11.5 + - - +
124A LEU* 3.2 21.2 + - + +
145A THR 3.1 15.9 - - - +
146A ASP* 4.6 10.8 - - - +
147A PHE* 3.4 35.8 - - + +
148A GLN* 4.7 6.7 - - - +
178A SER 5.7 2.6 + - - -
180A THR 4.2 4.5 + - - +
181A MET* 2.9 52.4 + - + +
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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