Contacts of the strand formed by residues 116 - 128 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B THR* 3.1 6.0 - - - -
113B ILE 2.8 39.0 + - - +
114B ASP 3.0 2.7 - - - -
115B GLY* 1.3 79.9 - - - +
117B THR* 1.3 63.1 + - - -
118B TYR* 3.4 11.5 - - - -
144B ARG* 3.9 20.4 - - - -
148B ARG* 6.1 0.2 - - - -
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Residues in contact with THR 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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110B GLN* 3.2 43.5 - - + +
111B VAL 3.4 7.6 - - - +
112B THR* 4.3 10.5 + - - +
116B GLY* 1.3 74.2 - - - -
118B TYR* 1.3 60.1 + - - +
144B ARG* 3.3 9.6 - - - +
145B THR* 2.9 44.7 + - + -
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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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93B ILE* 4.1 4.9 - - + -
94B VAL 4.0 2.9 - - - -
95B GLU* 2.6 35.3 + - - -
110B GLN* 3.2 8.6 - - - +
111B VAL* 2.8 48.4 + - + +
113B ILE* 3.3 26.9 + - + -
114B ASP* 5.0 2.1 + - - +
116B GLY* 3.4 15.9 - - - -
117B THR* 1.3 76.3 - - - +
119B ASP* 1.3 61.3 + - - +
120B ILE 4.0 0.2 + - - -
142B SER* 4.0 11.7 - - - -
143B VAL 3.3 15.0 - - - +
144B ARG* 3.4 36.3 + - + -
145B THR 4.7 0.2 - - - +
148B ARG* 3.7 11.3 + - - -
153B VAL* 4.7 2.4 - - - +
158B HIS* 3.8 31.7 + + + -
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Residues in contact with ASP 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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101B ARG* 2.6 30.8 + - - +
107B SER* 3.7 13.9 + - - +
109B GLY 3.4 2.4 - - - -
110B GLN* 3.0 36.2 + - - +
118B TYR* 1.3 73.4 - - - +
120B ILE* 1.3 61.4 + - - +
121B TYR* 3.3 33.0 - - + +
142B SER* 3.3 3.1 - - - -
143B VAL 2.8 29.9 + - - -
145B THR* 3.7 2.6 - - - +
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Residues in contact with ILE 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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107B SER* 3.6 1.2 - - - -
108B LEU* 2.7 36.4 + - + +
109B GLY 2.9 13.0 + - - +
111B VAL* 4.0 15.5 - - + -
118B TYR 4.7 0.2 - - - +
119B ASP* 1.3 74.6 - - - +
121B TYR* 1.3 67.1 + - - +
141B TRP 3.2 9.2 - - - +
142B SER* 4.0 14.6 - - - +
161B ALA* 3.7 30.3 - - + +
162B TRP* 3.7 18.4 - - + -
165B ARG* 3.6 38.8 - - - +
167B LEU* 4.1 17.3 - - + -
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Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.6 17.7 + - - -
102B PRO 4.4 2.5 + - - -
103B PRO* 3.5 43.5 - - + -
105B ALA* 3.3 33.0 - - + -
106B THR 3.4 15.7 - - - +
107B SER* 3.6 17.9 - - - -
108B LEU* 4.2 6.7 - - - -
119B ASP* 3.3 42.6 - - + +
120B ILE* 1.3 74.0 - - - +
122B ARG* 1.3 60.5 + - - +
140B TYR* 3.6 3.1 - - - -
141B TRP* 2.9 36.8 + - + +
143B VAL* 4.0 16.4 - - + -
167B LEU* 4.0 4.6 - - - +
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Residues in contact with ARG 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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105B ALA* 4.0 9.2 - - - +
106B THR 4.7 2.6 + - - +
108B LEU* 3.9 12.8 - - + +
121B TYR* 1.3 74.3 - - - +
123B THR* 1.3 74.2 + - - +
124B THR* 3.6 11.4 + - - +
138B ASP* 3.0 38.6 + - + -
139B GLN 3.4 8.3 - - - +
140B TYR* 4.3 6.5 - - + -
167B LEU* 3.7 30.8 - - + +
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Residues in contact with THR 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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103B PRO* 4.0 17.7 - - + +
104B GLY 5.3 0.4 - - - +
105B ALA* 3.6 22.9 - - + -
122B ARG* 1.3 81.4 - - - +
124B THR* 1.3 67.9 + - - +
138B ASP* 3.2 8.1 - - - +
139B GLN* 2.6 54.0 + - - +
141B TRP* 2.8 23.6 + - + +
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Residues in contact with THR 124 (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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122B ARG* 3.6 17.3 + - - +
123B THR* 1.3 79.0 - - - +
125B ARG* 1.3 78.8 + - - +
126B VAL* 4.5 8.1 + - + +
136B THR* 4.6 11.0 - - + -
137B PHE 3.6 9.2 - - - +
138B ASP* 2.8 23.7 + - - +
139B GLN* 4.9 0.2 - - - +
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Residues in contact with ARG 125 (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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18B TRP* 6.1 1.6 - - - -
43B ASN* 4.7 11.7 + - - -
90B GLU* 4.6 3.6 + - - -
124B THR* 1.3 76.5 - - - +
126B VAL* 1.3 62.2 + - - +
128B GLN* 3.0 44.8 + - + +
129B PRO* 4.8 4.2 - - - +
135B ALA 4.2 0.6 - - - +
136B THR* 3.2 7.1 - - - +
137B PHE* 2.8 57.5 + - + +
139B GLN* 3.4 41.7 - - + +
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Residues in contact with VAL 126 (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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124B THR* 4.6 9.6 - - + -
125B ARG* 1.3 76.0 - - - +
127B ASN* 1.3 87.5 + - + +
128B GLN* 3.0 19.4 + - - +
136B THR* 3.6 20.4 - - + +
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Residues in contact with ASN 127 (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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126B VAL* 1.3 89.6 - - + +
128B GLN* 1.3 67.0 + - - +
134B THR* 3.7 26.5 - - + +
135B ALA* 3.1 14.7 + - - -
136B THR* 3.1 15.9 + - - -
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Residues in contact with GLN 128 (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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125B ARG* 3.0 55.3 + - + +
126B VAL 3.0 26.2 + - - +
127B ASN* 1.3 83.0 + - - +
129B PRO* 1.3 83.4 - - + +
130B SER 3.5 0.2 + - - -
134B THR* 3.5 5.1 - - - -
135B ALA 2.8 27.9 + - - +
137B PHE* 3.9 12.1 - - + -
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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