Contacts of the strand formed by residues 165 - 173 (chain A) in PDB entry 1FXL
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 SER 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PRO 4.6 1.6 + - - -
134A LYS* 3.4 43.6 + - - +
136A MET 4.8 4.4 + - - -
156A ILE* 3.5 20.2 - - - +
157A LEU 3.9 6.1 - - - -
158A VAL* 4.0 9.5 - - - +
163A GLY 3.9 2.4 + - - -
164A VAL* 1.3 88.7 - - - +
166A ARG* 1.3 60.2 + - - +
167A GLY* 3.1 14.9 + - - -
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Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 4.0 16.9 + - - +
157A LEU* 2.9 31.6 + - - +
158A VAL 3.7 23.8 + - - -
159A ASP* 3.7 22.2 - - + +
160A GLN* 5.5 6.9 - - - +
164A VAL 4.0 0.9 - - - +
165A SER* 1.3 73.4 - - - +
167A GLY* 1.3 62.1 + - - +
168A VAL* 3.4 26.7 + - + +
3B U 2.5 48.3 + - - -
4B U 6.0 1.4 - - - -
5B U 5.8 1.4 + - - -
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Residues in contact with GLY 167 (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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130A SER* 3.4 1.6 - - - -
131A GLY 3.0 12.6 + - - -
132A LEU* 2.9 54.9 + - - +
133A PRO 4.7 0.7 - - - -
134A LYS* 4.3 5.6 - - - +
156A ILE* 5.2 1.1 - - - -
157A LEU 4.3 0.2 + - - -
165A SER* 3.1 14.9 + - - -
166A ARG* 1.3 79.7 - - - +
168A VAL* 1.3 57.6 + - - +
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Residues in contact with VAL 168 (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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128A TYR* 3.6 23.3 - - + +
129A VAL 3.1 7.6 - - - +
130A SER* 3.8 15.5 - - - -
131A GLY 4.7 0.9 - - - +
132A LEU* 4.5 4.7 - - - -
156A ILE* 3.6 5.6 - - - +
157A LEU* 2.8 48.4 + - + +
166A ARG* 3.6 37.7 - - + +
167A GLY* 1.3 85.3 - - - +
169A GLY* 1.3 58.7 + - - +
3B U 5.1 1.1 - - - +
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Residues in contact with GLY 169 (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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128A TYR* 3.6 5.4 - - - -
129A VAL* 2.8 37.0 + - - +
132A LEU* 4.6 6.1 - - - +
141A LEU* 5.4 1.8 - - - -
155A ARG 2.9 15.0 - - - -
156A ILE* 4.2 0.4 - - - -
157A LEU* 4.2 4.7 - - - -
168A VAL* 1.3 77.6 - - - +
170A PHE* 1.3 73.1 + - - -
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Residues in contact with PHE 170 (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 ASN* 3.8 15.7 - - - +
127A LEU 3.1 17.5 - - - +
128A TYR* 3.6 17.9 - + + -
129A VAL* 4.7 0.9 - - - +
141A LEU* 4.3 0.9 - - - +
153A THR* 5.2 2.5 - - - +
154A SER* 3.2 5.3 - - - -
155A ARG* 2.9 33.2 + - + +
157A LEU* 3.9 15.3 - - + -
169A GLY* 1.3 79.4 - - - -
171A ILE* 1.3 69.1 + - - +
203A ALA* 4.3 1.3 - - + -
3B U 3.1 47.3 - + - -
4B U 3.4 67.8 - + - +
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Residues in contact with ILE 171 (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 ALA 3.7 1.7 - - - +
126A ASN* 3.6 1.9 - - - -
127A LEU* 2.7 42.8 + - + +
129A VAL* 4.4 7.0 - - + -
141A LEU* 3.6 25.6 - - + +
142A GLU* 4.7 0.2 - - + -
145A PHE* 4.0 33.7 - - + -
151A ILE* 4.4 12.6 - - + -
153A THR 3.5 4.9 - - - +
154A SER* 3.4 27.4 - - - -
170A PHE* 1.3 78.0 - - - +
172A ARG* 1.3 63.8 + - - +
173A PHE* 3.7 32.7 + - + -
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Residues in contact with ARG 172 (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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116A ARG* 5.2 0.7 - - - +
122A ILE 5.6 3.4 + - - +
124A ASP* 5.4 3.8 - - - +
125A ALA* 3.4 15.6 - - + +
126A ASN* 3.6 40.1 + - - +
151A ILE* 3.6 2.3 - - - +
152A ILE* 2.6 49.6 + - - +
153A THR* 2.9 27.7 + - - +
171A ILE* 1.3 75.7 - - - +
173A PHE* 1.3 63.5 + - - +
4B U 4.5 4.0 + - - +
7B A 3.5 6.7 + - - -
8B U 2.7 73.1 + - - +
9B U 4.7 4.0 + - - -
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Residues in contact with PHE 173 (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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116A ARG* 4.3 1.2 + - - -
122A ILE 4.7 1.0 - - - +
125A ALA* 2.9 21.8 + - - +
127A LEU* 3.6 14.6 - - + -
145A PHE* 3.3 37.9 - + + -
148A TYR* 3.9 4.3 - - + -
149A GLY 3.6 25.6 - - - -
150A ARG 3.4 16.6 - - - -
151A ILE* 4.2 7.0 - - + -
152A ILE* 3.6 8.5 - - - +
171A ILE* 3.7 11.2 - - + -
172A ARG* 1.3 79.4 - - - +
174A ASP* 1.3 65.7 + - - +
175A LYS 3.7 17.9 - - - +
178A GLU* 3.8 10.8 - - + +
179A ALA* 3.6 18.8 - - + +
182A ALA* 3.6 30.5 - - + -
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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