Contacts of the strand formed by residues 113 - 122 (chain A) in PDB entry 4Y1W
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 GLY 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A TYR* 3.8 8.3 - - - -
112A LYS* 1.3 75.4 - - - +
114A THR* 1.3 62.0 + - - -
172A LYS* 3.7 13.4 - - - +
173A ILE* 2.7 38.5 + - - +
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Residues in contact with THR 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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111A TYR* 2.8 24.2 + - - -
113A GLY* 1.3 75.0 - - - -
115A ALA* 1.3 65.1 + - - +
116A TYR* 3.5 32.2 - - + +
145A THR* 4.1 10.2 - - - +
170A GLU* 3.8 21.1 - - + +
171A VAL 3.3 8.0 + - - +
172A LYS* 4.5 10.3 - - - +
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Residues in contact with ALA 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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111A TYR* 4.5 4.5 - - + -
113A GLY 4.1 0.2 + - - -
114A THR* 1.3 77.4 - - - +
116A TYR* 1.3 72.3 + - - +
143A THR* 3.5 24.9 - - + +
144A SER 3.4 16.2 - - - +
145A THR* 4.3 2.2 - - + +
170A GLU* 3.7 0.3 - - - -
171A VAL* 2.8 37.4 + - + +
173A ILE* 3.8 16.6 - - + -
192A VAL* 5.2 1.1 - - + -
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Residues in contact with TYR 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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23A ALA* 3.1 19.7 - - + +
24A ILE* 3.8 25.6 - - + -
114A THR* 3.5 23.6 - - + +
115A ALA* 1.3 77.5 - - - +
117A ARG* 1.3 61.3 + - - +
143A THR* 3.3 7.3 - - - -
144A SER 2.8 38.2 + - - +
145A THR 3.8 18.4 - - - -
147A PRO* 3.8 23.3 - - + -
150A ALA* 3.6 23.2 - - + +
169A PHE 3.3 15.0 - - - +
170A GLU* 3.0 37.4 + - + -
171A VAL* 4.8 0.7 - - - -
188A LYS* 5.0 0.7 + - - -
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Residues in contact with ARG 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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80A ARG* 6.1 1.2 - - - +
116A TYR* 1.3 77.2 - - - +
118A GLY* 1.3 71.0 + - - +
119A THR* 4.0 23.9 + - - +
137A GLU* 2.9 37.4 + - - +
139A ALA* 6.1 0.2 - - - +
140A PHE 5.2 3.2 + - - -
141A THR* 3.8 26.7 - - - +
142A SER 3.6 25.4 + - - +
143A THR* 4.2 6.3 - - + -
150A ALA* 3.9 8.3 - - - +
168A LEU* 3.6 2.2 - - - +
169A PHE* 2.8 48.6 + - + +
171A VAL* 5.0 2.9 - - + -
188A LYS* 6.0 0.7 - - - +
200A PHE* 5.5 2.2 - - - -
232A LEU* 3.7 18.6 - - - +
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Residues in contact with GLY 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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117A ARG* 1.3 80.7 + - - +
119A THR* 1.3 64.0 + - - -
150A ALA* 3.9 13.1 + - - +
153A PHE* 5.0 8.2 - - - +
154A SER* 3.7 23.7 - - - -
167A VAL 3.3 9.0 - - - -
168A LEU* 3.8 7.6 - - - -
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Residues in contact with THR 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 ARG* 4.0 25.4 + - - +
118A GLY* 1.3 77.0 - - - -
120A TRP* 1.3 76.6 + - - +
121A VAL* 3.7 13.7 - - + -
154A SER* 4.0 6.8 - - - -
166A ARG* 3.8 1.4 - - - +
167A VAL* 2.9 32.1 + - - +
169A PHE* 3.7 26.7 - - + -
232A LEU* 4.8 7.2 - - + -
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Residues in contact with TRP 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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119A THR* 1.3 86.1 + - - +
121A VAL* 1.3 62.8 + - - +
153A PHE 5.4 1.6 - - - -
154A SER* 3.2 36.8 + - - +
155A VAL 3.8 6.1 - - - -
156A VAL 3.1 29.9 + - - -
157A HIS* 3.6 34.1 - + + -
158A PRO* 3.9 21.8 - - + -
164A LEU* 4.0 28.8 - - + +
165A LYS* 3.4 12.1 - - - -
166A ARG* 3.4 41.1 - - + -
232A LEU 5.1 2.9 - - - +
233A TYR* 5.9 3.6 - - - -
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Residues in contact with VAL 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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119A THR* 3.7 18.8 - - + -
120A TRP* 1.3 79.7 - - - +
122A LYS* 1.3 76.0 + - - +
125A LEU* 3.9 27.4 - - + -
126A LEU* 4.5 9.6 - - + +
129A LEU* 5.4 4.3 - - + -
164A LEU* 3.4 4.4 - - - -
165A LYS* 2.8 31.9 + - - +
167A VAL* 3.6 29.2 - - + -
169A PHE* 4.5 3.6 - - + -
214A ILE* 6.2 1.1 - - + -
232A LEU* 4.0 22.9 - - + +
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A VAL* 1.3 77.0 - - - +
123A LEU* 1.3 66.5 + - - +
124A SER* 3.7 14.8 - - - +
125A LEU* 3.0 12.8 + - + +
126A LEU* 3.0 18.6 + - - +
160A SER* 6.1 0.4 - - - -
162A GLN* 3.5 35.5 - - + +
163A ARG 3.6 7.0 - - - +
164A LEU* 3.8 17.4 - - + +
232A LEU 5.4 1.8 + - - -
233A TYR 3.8 15.7 + - - +
234A SER* 2.9 34.9 + - - +
235A GLY* 4.6 3.6 - - - +
236A GLU* 5.7 0.2 + - - -
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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