Contacts of the strand formed by residues 114 - 123 (chain B) in PDB entry 4PSQ
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 TYR 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B TRP* 3.4 9.0 - - - -
108B ASP* 3.1 31.5 + - + -
109B THR* 2.7 42.2 + - - -
110B ASP* 3.1 41.1 + - - +
113B THR* 1.3 81.7 + - - +
115B ALA* 1.3 62.1 + - - +
116B VAL* 4.2 7.6 - - + -
137B PHE 3.4 7.2 - - - +
144B LEU* 3.8 17.7 - - + -
148B ALA* 3.7 18.8 - - + -
151B ILE* 3.3 27.2 - - + +
152B VAL* 3.9 19.3 - - + -
210B EDO 3.1 26.0 + - - -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.6 27.8 - - + -
24B TRP* 3.8 8.9 - - + -
106B ILE* 5.3 0.9 - - + -
108B ASP 3.5 7.6 - - - +
109B THR* 3.6 12.1 - - - +
114B TYR* 1.3 79.9 - - - +
116B VAL* 1.3 66.7 + - - +
117B GLN 4.1 0.4 - - - -
135B PHE 3.9 0.3 - - - +
136B VAL* 3.6 4.2 - - - +
137B PHE* 2.8 41.1 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 3.7 3.7 - - - +
107B VAL* 2.8 45.8 + - + -
108B ASP 2.9 13.7 + - - +
114B TYR* 4.3 9.0 - - + -
115B ALA* 1.3 79.0 - - - +
117B GLN* 1.3 65.1 + - - +
134B SER* 4.2 7.4 - - - +
135B PHE 3.6 6.5 - - - +
136B VAL* 5.0 4.9 - - + -
152B VAL* 4.0 37.5 - - + +
155B ARG* 4.4 15.5 - - + -
156B GLN* 5.5 3.1 - - + -
159B LEU* 4.2 13.2 - - + -
165B TYR* 4.6 3.6 - - - +
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 6.3 0.2 - - + -
104B HIS* 3.6 39.3 + - + +
105B TRP 3.4 9.0 - - - +
106B ILE* 4.7 7.0 - - + +
107B VAL* 4.2 0.4 - - - -
115B ALA 4.1 0.6 - - - -
116B VAL* 1.3 75.9 - - - +
118B TYR* 1.3 85.6 + - - +
119B SER* 3.9 3.2 - - - -
133B TYR* 3.5 24.8 + - - -
134B SER* 2.6 34.3 + - - -
135B PHE* 2.9 42.9 + - - +
137B PHE* 3.8 23.6 - - + -
201B 2WL 4.9 0.4 - - - +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.9 4.1 - - + +
9B PHE* 3.7 25.9 - + - -
104B HIS* 3.9 0.3 - - - -
105B TRP* 3.0 56.1 + + + +
107B VAL* 3.4 20.4 - - + -
117B GLN* 1.3 81.2 + - - +
119B SER* 1.3 75.5 + - - +
120B CYS* 3.8 19.7 - - + -
129B CYS* 3.3 30.5 - - - +
132B SER* 3.9 14.9 - - - -
133B TYR 3.5 9.2 - - - -
134B SER* 4.4 1.1 - - - -
159B LEU* 4.0 32.5 + - + -
161B LEU* 4.0 22.7 - - + -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASP* 3.8 8.8 - - - +
103B ASP* 2.6 33.4 + - - -
105B TRP* 5.8 0.4 - - - -
117B GLN* 3.9 2.2 - - - -
118B TYR* 1.3 80.5 - - - +
120B CYS* 1.3 64.0 + - - +
121B ARG* 4.0 1.3 + - - +
132B SER* 3.2 5.4 - - - -
133B TYR* 2.9 70.3 + - - +
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Residues in contact with CYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.9 19.5 - - + -
103B ASP* 3.6 18.8 + - - +
105B TRP* 6.2 1.0 - - + -
118B TYR* 3.8 15.7 - - + +
119B SER* 1.3 73.1 + - - +
121B ARG* 1.3 58.7 + - - +
122B LEU 3.3 21.3 - - - -
123B LEU* 4.0 6.7 - - - -
129B CYS* 2.0 50.7 - - - -
131B ASP 3.7 0.2 - - - -
206B EDO 3.3 21.0 + - - -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO* 3.4 27.0 - - - +
33B GLU 4.0 9.3 + - - -
35B LEU 5.3 0.4 + - - -
36B PHE* 4.5 0.4 - - - -
90B TYR* 3.3 5.5 + - - -
102B ASP* 3.0 42.8 + - - +
103B ASP 6.2 0.2 - - - +
119B SER* 4.0 4.7 - - - +
120B CYS* 1.3 75.7 - - - +
122B LEU* 1.3 65.3 + - + +
131B ASP* 2.8 34.5 + - - +
133B TYR* 3.6 21.3 - - + -
201B 2WL 2.8 40.4 + - - -
206B EDO 4.0 15.4 + - - -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B CYS* 3.3 11.8 - - - -
121B ARG* 1.3 83.6 - - + +
123B LEU* 1.3 65.2 + - - +
130B ALA* 2.7 44.2 + - + -
131B ASP* 3.4 18.0 + - + +
206B EDO 4.5 3.1 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.6 27.6 - - + -
120B CYS* 4.0 7.4 - - - -
122B LEU* 1.3 85.6 - - - +
124B ASN* 1.3 68.1 + - - +
127B GLY* 3.4 30.7 - - - +
128B THR 3.5 2.2 - - - +
130B ALA* 4.2 3.4 - - - +
206B EDO 4.1 24.3 - - - +
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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