Contacts of the strand formed by residues 130 - 141 (chain A) in PDB entry 4IF8
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 LEU 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.8 16.4 - - + +
125A GLN* 3.5 36.2 - - + +
127A THR* 2.9 35.6 + - - +
129A ASP* 1.3 78.7 - - - +
131A LYS* 1.3 63.0 + - - +
132A LEU* 4.0 14.4 - - + -
210A PHE* 3.7 31.4 - - + -
211A ARG 3.4 15.9 - - - +
212A ALA* 3.9 4.9 - - + -
266A LYS* 3.8 17.7 - - + -
268A ILE* 3.8 23.3 - - + -
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Residues in contact with LYS 131 (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 GLN 3.2 4.7 - - - +
126A LYS* 4.0 25.6 - - + +
127A THR 3.3 25.4 + - - +
128A GLN* 4.7 8.1 + - - +
130A LEU* 1.3 70.9 - - - +
132A LEU* 1.3 59.3 + - - +
188A LYS* 4.8 12.1 - - - +
209A PHE* 3.9 15.1 - - + +
210A PHE* 3.4 4.5 - - - -
211A ARG* 2.8 58.9 + - + +
363A ARG* 5.8 3.4 - - - +
501A SO4 5.6 1.6 - - - +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.6 39.9 - - + +
124A THR* 3.3 7.8 - - - +
125A GLN 3.0 26.9 + - - +
130A LEU* 4.0 14.8 - - + -
131A LYS* 1.3 75.8 - - - +
133A SER* 1.3 69.2 + - - +
134A ILE* 4.0 26.0 - - + -
208A ILE* 4.2 11.7 - - + -
209A PHE* 3.5 12.3 - - - +
210A PHE* 4.1 13.2 - - + -
403A LEU* 3.8 31.2 - - + -
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Residues in contact with SER 133 (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 14.0 - - - +
125A GLN 4.9 2.3 + - - -
132A LEU* 1.3 76.9 + - - +
134A ILE* 1.3 65.7 - - - +
135A GLY 4.0 0.4 - - - -
207A TYR 3.9 0.9 - - - +
208A ILE* 3.4 24.3 - - - +
209A PHE* 3.4 41.3 + - - -
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Residues in contact with ILE 134 (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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77A LEU* 3.8 33.0 - - + -
78A SER* 3.7 15.9 - - - +
81A THR* 3.5 26.9 - - + +
120A ILE* 4.4 33.0 - - + +
123A LEU* 4.7 6.3 - - + -
124A THR* 4.6 5.8 + - - +
132A LEU* 4.0 12.8 - - + +
133A SER* 1.3 77.0 - - - +
135A GLY* 1.3 60.6 + - - +
136A ASN* 3.9 10.0 + - - +
158A TYR 4.8 8.9 - - - +
159A SER* 5.3 6.1 - - - +
184A LYS* 5.4 0.3 + - - -
206A ASN* 4.4 0.4 - - - +
207A TYR 3.6 3.1 - - - -
208A ILE* 3.8 23.6 - - + -
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Residues in contact with GLY 135 (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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133A SER* 4.0 1.4 - - - -
134A ILE* 1.3 73.8 - - - +
136A ASN* 1.3 59.6 + - - -
159A SER 5.9 0.7 - - - -
184A LYS* 4.3 8.3 - - - -
206A ASN* 3.3 12.5 + - - -
207A TYR* 2.7 65.7 + - - -
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Residues in contact with ASN 136 (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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81A THR* 3.0 31.2 + - - -
82A ALA* 3.3 22.2 - - - +
85A MET* 4.3 9.6 - - + -
120A ILE* 5.3 0.4 - - - +
134A ILE* 3.9 10.3 + - - +
135A GLY* 1.3 71.8 + - - -
137A THR* 1.3 62.5 + - - +
138A LEU 4.2 0.2 - - - -
158A TYR* 4.8 13.1 + - - +
159A SER 5.1 1.8 + - - -
160A ALA* 3.2 24.9 - - + +
161A GLU* 3.0 27.6 + - - +
184A LYS* 4.8 0.2 - - - +
204A LEU* 4.5 4.2 - - - +
205A ALA 3.5 3.1 - - - -
206A ASN* 2.8 24.0 + - - +
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Residues in contact with THR 137 (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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136A ASN* 1.3 71.7 - - - +
138A LEU* 1.3 62.8 + - - +
139A PHE* 3.5 34.9 + - + -
161A GLU* 2.8 25.2 + - + +
163A ILE* 3.7 23.6 - - + -
180A PHE* 4.0 4.7 - - + -
203A LEU 3.7 0.7 - - - +
204A LEU* 3.7 4.6 - - - +
205A ALA* 2.9 36.8 + - - +
207A TYR* 2.6 30.3 + - - -
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Residues in contact with LEU 138 (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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85A MET* 4.4 7.8 - - + +
86A LEU* 4.2 17.9 - - + -
136A ASN 4.2 0.4 - - - -
137A THR* 1.3 72.9 - - - +
139A PHE* 1.3 60.4 + - - +
140A ILE* 4.2 14.4 - - + -
150A PHE* 3.6 36.8 - - + -
161A GLU 2.9 7.4 + - - +
162A THR* 3.2 17.3 - - - +
163A ILE 2.9 25.1 + - - +
202A MET* 3.8 29.6 - - + -
203A LEU 3.4 2.5 - - - +
204A LEU* 3.9 32.3 - - + -
341A ILE* 4.5 1.1 - - + -
349A VAL* 5.1 1.8 - - + -
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Residues in contact with PHE 139 (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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137A THR* 3.5 33.0 - - + -
138A LEU* 1.3 72.8 - - - +
140A ILE* 1.3 59.7 + - - +
163A ILE* 3.3 32.8 - - + -
165A THR* 3.4 21.5 - - - +
167A PHE* 3.4 17.0 - - + -
176A GLN* 4.5 3.1 - - - -
177A ILE* 3.6 48.9 - - + -
180A PHE* 3.7 22.2 - + + -
181A ILE* 4.1 10.3 - - + -
202A MET* 3.3 3.6 - - - -
203A LEU* 2.7 52.1 + - + +
205A ALA* 4.1 3.4 - - + -
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Residues in contact with ILE 140 (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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138A LEU* 4.2 8.1 - - + -
139A PHE* 1.3 79.2 - - - +
141A ASP* 1.3 77.4 + - - +
144A LEU* 3.7 27.1 - - + -
146A PRO* 4.3 14.8 - - + -
162A THR* 3.6 34.3 - - + +
163A ILE 3.0 6.3 + - - -
164A LEU* 3.3 9.8 - - + +
165A THR 2.9 19.6 + - - -
167A PHE* 3.9 3.8 - - - -
201A VAL 3.4 3.8 - - - +
202A MET* 3.7 31.6 - - + -
341A ILE* 3.8 18.2 - - + -
342A ALA* 5.3 2.9 - - + -
347A LEU* 5.7 0.2 - - + -
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Residues in contact with ASP 141 (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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140A ILE* 1.3 75.5 - - - +
142A GLN* 1.4 53.9 + - - +
143A ARG* 3.0 50.7 + - - +
144A LEU* 2.9 37.4 + - + +
164A LEU* 4.3 1.2 - - - +
165A THR 3.3 5.1 - - - +
167A PHE* 3.1 38.8 + - + +
168A GLN* 4.3 3.1 + - - +
201A VAL* 2.9 38.8 + - + +
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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