Contacts of the strand formed by residues 116 - 127 (chain A) in PDB entry 1F6O
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 GLU 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A VAL* 4.3 9.2 - - + -
109A ARG 3.2 5.6 - - - +
110A ARG* 4.1 18.8 + - + +
114A GLY 3.8 9.6 - - - +
115A THR* 1.3 81.8 - - - +
117A LEU* 1.3 66.6 + - - +
118A ARG* 2.6 36.1 + - - +
188A GLU* 3.8 18.5 - - - +
189A GLY* 4.5 1.4 + - - -
243A TRP* 3.1 27.7 - - - -
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Residues in contact with LEU 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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107A LEU 3.5 0.9 - - - +
108A VAL* 3.2 6.1 - - - +
109A ARG* 2.7 42.5 + - + +
111A LEU* 3.9 24.9 - - + -
115A THR* 4.0 7.6 - - + -
116A GLU* 1.3 76.6 - - - +
118A ARG* 1.3 60.4 + - - +
188A GLU 3.3 3.6 - - - +
189A GLY* 3.6 33.7 - - - +
192A THR* 4.0 15.0 - - + -
193A MET* 4.2 2.7 - - + -
196A LEU* 4.2 7.0 - - + -
224A ALA 3.5 25.1 - - - +
225A LEU* 3.7 31.6 - - + +
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Residues in contact with ARG 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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80A LYS* 3.6 30.7 - - - +
81A GLY* 4.6 3.2 - - - +
106A VAL* 3.8 14.1 - - + -
107A LEU 3.3 2.5 - - - -
108A VAL* 2.8 24.6 - - + +
116A GLU* 2.6 35.0 + - - +
117A LEU* 1.3 81.0 - - - +
119A GLY* 1.3 59.1 + - - +
187A LEU* 2.9 28.6 + - + -
188A GLU* 3.0 50.1 + - + +
193A MET* 3.6 11.1 - - - +
225A LEU* 5.5 0.4 - - - -
243A TRP* 4.5 1.6 - - - -
245A GLU* 2.5 47.0 + - - -
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Residues in contact with GLY 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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106A VAL* 3.5 5.0 - - - +
107A LEU* 2.9 36.6 + - - +
118A ARG* 1.3 75.9 - - - +
120A ARG* 1.3 64.1 + - - -
121A ILE 3.5 1.0 + - - -
184A LEU* 4.2 20.2 - - - +
185A GLU 3.3 13.0 - - - -
186A PRO* 4.5 1.8 - - - -
187A LEU 4.3 0.2 - - - -
193A MET* 5.1 2.0 - - - -
225A LEU* 5.2 0.8 - - - +
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Residues in contact with ARG 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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104A GLY* 2.9 32.1 + - - +
105A GLN 3.4 14.8 - - - +
106A VAL* 4.4 4.0 - - + +
119A GLY* 1.3 71.1 - - - -
121A ILE* 1.3 66.1 + - - +
122A VAL* 3.3 2.9 + - + +
184A LEU* 3.2 2.2 - - - -
185A GLU* 2.6 64.4 + - + +
187A LEU* 3.7 19.0 - - + +
247A GLY 4.6 0.4 - - - -
248A PRO* 3.5 43.7 + - - +
250A GLU* 3.8 24.0 + - - +
254A PRO* 5.9 2.6 - - - +
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Residues in contact with ILE 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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102A PHE* 3.5 32.8 - - + +
103A LEU* 3.6 3.4 - - + +
104A GLY* 3.0 22.5 + - - -
105A GLN 3.0 11.7 + - - +
107A LEU* 4.7 4.0 - - + -
119A GLY 4.6 2.5 - - - +
120A ARG* 1.3 71.3 - - - +
122A VAL* 1.3 62.7 + - - +
123A GLU 4.1 5.8 - - - +
124A THR* 3.5 31.0 - - + -
181A LEU* 3.8 27.4 - - + -
183A ALA 4.3 1.8 - - - +
184A LEU* 3.5 22.7 - - + -
244A LEU* 3.9 26.2 - - + -
279A VAL* 4.5 1.7 - - - +
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Residues in contact with VAL 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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103A LEU* 3.8 5.8 - - - +
120A ARG* 3.7 11.4 - - + +
121A ILE* 1.3 78.1 - - - +
123A GLU* 1.3 59.6 + - - +
183A ALA* 2.9 37.1 + - + +
184A LEU* 4.0 1.1 - - - +
185A GLU* 4.0 18.4 - - + +
278A TYR* 2.9 28.8 - - - +
279A VAL* 3.0 22.4 + - + -
282A SER* 3.8 21.3 - - - +
284A TRP* 3.9 24.2 - - + -
285A VAL* 4.0 2.9 - - + +
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Residues in contact with GLU 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 LEU* 4.0 0.2 - - - +
121A ILE* 3.8 3.2 - - - +
122A VAL* 1.3 80.2 - - - +
124A THR* 1.3 71.0 + - - +
181A LEU* 3.9 1.9 - - - -
182A ARG* 2.5 58.0 + - + -
183A ALA* 3.3 21.3 + - + +
276A ARG* 2.8 36.6 + - - +
277A PHE 3.3 7.0 - - - +
278A TYR* 3.9 9.4 - - + -
285A VAL* 3.7 4.3 - - + -
286A SER* 2.7 34.5 + - - -
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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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99A ALA* 2.8 34.1 + - - +
102A PHE* 3.9 9.4 - - + -
103A LEU* 3.6 5.7 - - + +
121A ILE* 3.5 23.8 - - + -
123A GLU* 1.3 80.5 - - - +
125A GLU* 1.3 62.1 + - - +
179A VAL* 4.1 8.3 - - + -
180A LEU 3.2 12.6 - - - +
181A LEU* 4.5 5.6 - - + -
182A ARG* 4.6 2.7 - - - +
276A ARG* 3.4 5.4 - - - +
277A PHE* 2.6 51.2 + - - +
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Residues in contact with GLU 125 (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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99A ALA* 4.3 4.3 - - - -
124A THR* 1.3 79.2 - - - +
126A ALA* 1.3 61.6 + - - +
127A TYR* 2.4 41.8 + - + -
179A VAL* 3.3 5.7 - - - -
180A LEU* 2.8 46.4 + - + +
182A ARG* 2.9 30.0 + - - -
261A ARG* 3.3 25.8 - - + +
262A VAL* 3.0 24.3 + - - +
275A LEU 3.3 3.8 - - - +
276A ARG* 3.7 10.6 - - + -
277A PHE* 4.8 0.2 - - - -
7D YRR 4.4 2.4 + - - -
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Residues in contact with ALA 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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95A ALA* 3.7 32.1 - - + +
96A VAL* 3.9 16.2 - - + +
99A ALA* 4.1 3.5 - - + +
125A GLU* 1.3 72.4 - - - +
127A TYR* 1.3 61.5 + - - +
128A LEU* 4.0 2.2 - - + -
132A ASP* 3.8 0.5 - - - +
178A CYS 3.9 3.8 - - - -
261A ARG* 2.9 26.3 + - - -
275A LEU* 2.8 24.9 + - + +
277A PHE* 4.1 8.5 - - + -
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Residues in contact with TYR 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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95A ALA* 4.0 1.2 - - - +
125A GLU* 2.4 48.9 + - + -
126A ALA* 1.3 74.1 - - - +
128A LEU* 1.3 60.2 + - - +
129A GLY 3.2 4.6 + - - -
132A ASP* 3.4 2.2 - - - -
134A ALA* 3.9 20.2 - - + -
135A ALA* 3.8 28.0 - - + -
149A MET* 4.7 1.8 - - + -
169A ASN* 4.9 2.2 - - - -
176A GLY 4.0 0.2 - - - +
177A ALA* 3.1 8.7 - - - +
178A CYS* 2.9 51.3 + - - +
180A LEU* 3.9 16.6 - - + -
261A ARG* 3.1 25.1 + - - -
264A VAL* 3.8 8.8 - - + +
7D YRR 3.4 24.0 + - - -
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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