Contacts of the strand formed by residues 116 - 128 (chain A) in PDB entry 1F5J
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A THR* 3.2 6.1 - - - -
113A ILE 2.9 33.9 + - - +
114A ASP 3.1 3.6 + - - -
115A GLY* 1.3 80.3 - - - +
117A THR* 1.3 61.8 + - - -
118A TYR* 3.4 13.0 - - - -
144A ARG* 4.0 17.3 - - - -
199B SER* 3.4 6.3 - - - -
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Residues in contact with THR 117 (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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110A GLN* 3.6 26.5 - - + +
111A VAL 3.4 9.6 - - - +
112A THR* 4.5 8.8 + - - +
116A GLY* 1.3 72.4 - - - -
118A TYR* 1.3 61.7 + - - +
144A ARG* 3.3 7.9 - - - +
145A THR* 2.8 55.6 + - + -
199B SER* 3.1 17.2 + - - -
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Residues in contact with TYR 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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93A ILE* 4.2 4.5 - - + -
94A VAL 3.9 3.4 - - - -
95A GLU* 2.6 35.5 + - - -
109A GLY 3.8 0.2 - - - +
110A GLN* 3.1 6.9 - - - -
111A VAL* 2.9 46.0 + - + +
113A ILE* 3.4 27.4 + - + -
114A ASP* 5.1 1.4 + - - +
116A GLY* 3.4 18.6 - - - -
117A THR* 1.3 75.2 - - - +
119A ASP* 1.3 63.6 + - - +
142A SER* 4.0 11.4 - - - +
143A VAL 3.3 15.0 - - - +
144A ARG* 3.3 40.3 + - + -
145A THR* 4.7 0.4 - - - +
148A ARG* 3.7 10.2 + - - -
153A VAL* 4.7 1.6 - - - +
158A HIS* 3.8 30.7 + + - -
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Residues in contact with ASP 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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101A ARG* 2.8 28.0 + - - +
107A SER* 3.0 19.9 + - - +
109A GLY 3.4 2.9 - - - -
110A GLN* 2.9 36.7 + - - +
118A TYR* 1.3 73.0 - - - +
120A ILE* 1.3 61.7 + - - +
121A TYR* 3.2 34.5 - - + +
142A SER* 3.3 2.9 - - - -
143A VAL 2.9 30.1 + - - -
145A THR* 3.8 0.7 - - - +
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Residues in contact with ILE 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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107A SER* 3.5 1.2 - - - -
108A LEU* 2.7 43.1 + - + +
109A GLY 2.8 15.7 + - - +
111A VAL* 3.9 24.0 - - + -
118A TYR 4.7 0.2 - - - +
119A ASP* 1.3 75.5 - - - +
121A TYR* 1.3 66.1 + - - +
141A TRP 3.2 8.7 - - - +
142A SER* 4.2 7.9 - - - +
161A ALA* 3.9 22.7 - - + +
162A TRP* 3.7 21.8 - - + -
165A ARG* 3.5 30.3 - - - +
167A LEU* 3.9 18.8 - - + -
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Residues in contact with TYR 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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101A ARG* 3.6 14.7 + - - -
102A PRO 4.2 2.0 + - - -
103A PRO* 3.4 42.2 - - + -
105A ALA* 3.3 31.6 - - + -
106A THR 3.5 11.9 - - - +
107A SER* 3.5 17.5 - - - -
108A LEU* 4.3 8.3 - - - -
119A ASP* 3.2 44.1 - - + +
120A ILE* 1.3 73.4 - - - +
122A ARG* 1.3 61.3 + - - +
140A TYR* 3.5 3.5 - - - -
141A TRP* 2.8 42.4 + - + +
143A VAL* 3.8 17.7 - - + -
167A LEU* 3.9 4.5 - - - +
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Residues in contact with ARG 122 (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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105A ALA* 3.9 10.0 - - - +
106A THR 4.8 2.2 + - - +
108A LEU* 4.0 13.7 - - + +
121A TYR* 1.3 75.3 - - - +
123A THR* 1.3 73.9 + - - +
124A THR* 3.7 10.9 + - - +
138A ASP* 2.9 40.1 + - + -
139A GLN 3.4 9.0 - - - +
140A TYR* 4.4 6.5 - - + -
167A LEU* 3.8 29.7 - - + +
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Residues in contact with THR 123 (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 PRO* 4.0 16.8 - - + +
104A GLY 5.5 0.2 - - - +
105A ALA* 3.8 20.6 - - + -
122A ARG* 1.3 80.5 - - - +
124A THR* 1.3 67.9 + - - +
125A ARG* 6.0 0.2 - - - -
138A ASP* 3.2 8.3 - - - +
139A GLN* 2.6 54.3 + - - +
141A TRP* 2.9 22.2 + - + +
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Residues in contact with THR 124 (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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122A ARG* 3.7 16.0 + - - +
123A THR* 1.3 77.3 + - - +
125A ARG* 1.3 79.7 + - - +
126A VAL* 4.3 13.0 - - + +
136A THR* 4.6 7.6 - - + -
137A PHE 3.6 8.7 - - - +
138A ASP* 2.7 23.3 + - - +
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Residues in contact with ARG 125 (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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43A ASN* 5.2 7.1 + - - -
90A GLU* 2.9 31.7 + - - -
92A TYR* 5.5 0.6 + - - -
124A THR* 1.3 78.0 - - - +
126A VAL* 1.3 62.4 + - - +
128A GLN* 3.5 42.9 + - + +
129A PRO* 4.5 7.7 + - - +
135A ALA 4.0 0.4 - - - +
136A THR* 3.2 7.1 - - - +
137A PHE* 2.8 54.4 + - + +
139A GLN* 3.1 38.6 - - + +
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Residues in contact with VAL 126 (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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124A THR* 4.5 10.8 - - + -
125A ARG* 1.3 74.7 - - - +
127A ASN* 1.3 89.7 + - + +
128A GLN* 3.1 18.5 + - - +
136A THR* 3.6 18.2 - - + +
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Residues in contact with ASN 127 (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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126A VAL* 1.3 90.7 - - + +
128A GLN* 1.3 66.7 + - - +
129A PRO* 4.9 0.2 - - - +
134A THR* 3.7 26.1 - - + +
135A ALA* 3.1 11.4 + - - -
136A THR* 3.0 15.8 + - - -
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Residues in contact with GLN 128 (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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125A ARG* 3.5 55.3 + - + +
126A VAL 3.1 23.5 + - - +
127A ASN* 1.3 83.1 + - - +
129A PRO* 1.3 83.5 - - + +
133A GLY 3.8 0.2 - - - +
134A THR* 3.4 4.6 - - - -
135A ALA 2.8 31.2 + - - +
137A PHE* 4.0 3.0 - - + -
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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