Contacts of the strand formed by residues 130 - 141 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B LEU* 4.1 13.0 - - + +
125B GLN* 3.5 37.4 - - + +
127B THR* 2.8 40.0 + - - +
128B GLN 3.5 1.8 + - - -
129B ASP* 1.4 79.1 - - - +
131B LYS* 1.3 60.9 + - - +
132B LEU* 4.0 11.7 - - + -
210B PHE* 3.5 34.8 - - + -
211B ARG 3.7 3.1 - - - -
212B ALA* 3.8 11.2 - - + -
266B LYS* 4.1 18.4 - - + -
268B ILE* 3.8 22.0 - - + -
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Residues in contact with LYS 131 (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 GLN 3.4 2.2 - - - +
126B LYS* 3.9 37.0 - - + +
127B THR 4.0 11.6 + - - +
128B GLN* 6.3 0.2 - - - +
130B LEU* 1.3 72.8 - - - +
132B LEU* 1.3 61.3 + - - +
133B SER* 5.7 2.2 - - - +
188B LYS* 6.1 1.8 - - - -
209B PHE* 3.9 27.4 - - + -
210B PHE* 3.4 5.5 - - - -
211B ARG* 2.8 53.9 + - + +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.6 37.7 - - + +
124B THR* 3.3 11.6 - - + -
125B GLN 2.9 31.4 + - - +
130B LEU* 4.0 14.1 - - + -
131B LYS* 1.3 73.7 - - - +
133B SER* 1.3 66.8 + - - +
134B ILE* 4.1 26.7 - - + -
208B ILE* 4.1 14.4 - - + -
209B PHE 3.3 4.0 - - - +
210B PHE* 3.8 28.0 - - + -
268B ILE* 4.8 0.2 - - + -
403B LEU* 3.9 22.7 - - + -
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Residues in contact with SER 133 (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* 4.3 3.8 - - - -
125B GLN 5.2 0.7 + - - -
131B LYS* 5.2 2.1 - - - +
132B LEU* 1.3 76.1 + - - +
134B ILE* 1.3 63.5 + - - +
135B GLY 4.1 0.7 - - - -
188B LYS* 6.0 0.3 + - - -
207B TYR* 4.3 21.5 - - - -
208B ILE* 3.2 9.5 - - - +
209B PHE* 3.0 45.5 + - - +
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Residues in contact with ILE 134 (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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77B LEU* 3.8 31.9 - - + -
78B SER* 3.6 20.0 - - - +
81B THR* 3.7 21.3 - - + +
120B ILE* 4.7 26.2 - - + +
123B LEU* 5.4 2.5 - - + -
124B THR* 4.0 18.8 - - + +
132B LEU* 4.1 10.8 - - + -
133B SER* 1.3 78.5 - - - +
135B GLY* 1.3 61.6 + - - +
136B ASN* 3.8 11.9 + - - +
158B TYR 5.3 5.0 - - - +
159B SER* 5.5 3.5 - - - +
184B LYS* 5.4 1.6 + - - -
206B ASN* 4.3 0.7 - - - +
207B TYR* 3.4 2.7 - - - -
208B ILE* 4.0 19.7 - - + -
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Residues in contact with GLY 135 (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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134B ILE* 1.3 74.5 - - - +
136B ASN* 1.3 60.7 + - - -
137B THR* 5.0 0.9 - - - -
184B LYS* 4.0 11.0 - - - -
205B ALA 4.2 2.2 - - - -
206B ASN* 3.3 11.3 + - - -
207B TYR* 2.8 63.1 + - - -
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Residues in contact with ASN 136 (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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81B THR* 3.0 31.8 + - - -
82B ALA* 3.3 22.5 - - - +
85B MET* 4.6 7.6 - - + -
120B ILE* 5.2 1.2 - - - +
134B ILE* 3.8 11.1 + - - +
135B GLY* 1.3 68.5 - - - -
137B THR* 1.3 61.6 + - - +
158B TYR* 4.8 13.4 + - + +
159B SER 4.4 2.5 + - - +
160B ALA* 3.2 36.6 - - + +
161B GLU* 3.1 15.4 + - - +
184B LYS* 4.9 0.2 - - - +
204B LEU* 4.5 3.3 - - + +
205B ALA 3.5 2.6 - - - +
206B ASN* 2.7 26.9 + - - +
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Residues in contact with THR 137 (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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135B GLY 5.0 0.5 - - - -
136B ASN* 1.3 74.2 + - - +
138B LEU* 1.3 62.8 + - - +
139B PHE* 3.4 36.2 + - + -
161B GLU* 2.9 21.1 + - - +
163B ILE* 3.7 17.7 - - + -
180B PHE* 3.6 22.3 - - + -
181B ILE* 3.9 12.8 - - - +
184B LYS* 4.2 5.2 - - - +
203B LEU 3.7 1.4 - - - +
204B LEU* 3.6 5.9 - - - +
205B ALA 2.9 34.2 + - - -
207B TYR* 5.8 0.2 - - - -
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Residues in contact with LEU 138 (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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85B MET* 4.7 10.7 - - + +
86B LEU* 4.1 21.1 - - + -
136B ASN 4.2 0.2 - - - -
137B THR* 1.3 73.1 - - - +
139B PHE* 1.3 61.3 + - - +
140B ILE 3.8 0.7 + - - -
150B PHE* 3.7 35.9 - - + -
160B ALA* 6.3 0.2 - - + -
161B GLU 2.9 11.6 + - - +
162B THR* 3.2 15.6 - - + +
163B ILE* 2.9 24.3 + - - +
202B MET* 3.8 39.9 - - + -
203B LEU 3.9 8.3 - - - +
204B LEU* 4.1 18.6 - - + -
341B ILE* 4.3 4.9 - - + -
349B VAL* 5.1 2.5 - - + -
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Residues in contact with PHE 139 (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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137B THR* 3.4 34.5 - - + -
138B LEU* 1.3 71.7 - - - +
140B ILE* 1.3 58.6 + - - +
163B ILE* 3.4 17.9 - - + -
165B THR* 3.4 19.7 - - + +
167B PHE* 3.6 15.8 - - + -
176B GLN* 4.7 1.6 - - + -
177B ILE* 3.7 42.6 - - + -
180B PHE* 3.8 31.0 - + + -
181B ILE* 4.0 3.6 - - + -
202B MET* 3.2 7.4 - - - +
203B LEU* 2.9 52.2 + - + +
205B ALA* 4.0 13.7 - - + -
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Residues in contact with ILE 140 (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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138B LEU* 5.0 0.9 - - + +
139B PHE* 1.3 74.8 - - - +
141B ASP* 1.3 71.9 + - - +
142B GLN 3.2 0.2 + - - -
144B LEU* 4.3 10.8 - - + -
146B PRO* 4.1 11.0 - - + -
162B THR* 3.8 26.7 - - + -
163B ILE 2.9 12.3 + - - +
164B LEU* 3.4 19.0 - - + -
165B THR* 2.8 23.2 + - - -
167B PHE* 3.9 3.1 - - - -
201B VAL 3.5 8.7 - - - +
202B MET* 3.8 15.7 - - + -
341B ILE* 3.8 28.9 - - + -
342B ALA* 3.8 22.2 - - + -
347B LEU* 4.4 3.6 - - + -
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Residues in contact with ASP 141 (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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140B ILE* 1.3 76.5 - - - +
142B GLN* 1.3 58.1 + - - +
143B ARG* 2.8 60.4 + - - +
144B LEU* 2.9 43.2 + - + +
145B GLN 4.5 0.9 + - - -
164B LEU* 4.6 0.9 - - - +
165B THR 3.3 6.1 - - - -
167B PHE* 3.2 28.0 + - + +
168B GLN* 3.7 1.0 + - - -
201B VAL* 2.8 29.7 + - + +
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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