Contacts of the strand formed by residues 157 - 168 (chain A) in PDB entry 4GFU
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 PHE 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LEU* 4.0 7.9 - - + -
78A LEU* 5.3 1.1 - - + -
113A LEU* 3.6 30.7 - - + -
116A TRP* 3.7 30.5 - + + -
117A ARG* 4.0 14.1 - - + -
120A TRP* 3.7 25.4 - + + -
152A LEU 4.4 0.2 - - - -
153A GLN* 3.0 10.8 + - - -
154A THR* 2.8 36.2 + - - +
156A LEU* 1.3 79.8 - - + +
158A CYS* 1.3 60.0 + - - +
159A ILE* 4.1 12.1 - - + -
178A VAL* 3.9 17.3 - - + -
179A THR 3.4 0.9 - - - -
180A PHE* 3.5 50.0 - + + -
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Residues in contact with CYS 158 (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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151A PRO* 4.5 13.9 - - - -
152A LEU 3.6 4.3 - - - -
153A GLN* 3.6 18.8 - - - +
156A LEU 4.0 0.4 + - - +
157A PHE* 1.3 74.8 - - - +
159A ILE* 1.3 61.6 - - - +
160A THR* 4.0 16.8 + - - -
177A LYS 3.4 4.7 - - - +
178A VAL* 3.6 0.5 - - - -
179A THR* 2.9 51.7 + - + +
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Residues in contact with ILE 159 (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 TRP* 3.7 46.9 - - + +
144A TYR 4.3 3.6 - - - +
146A ALA 4.0 21.9 - - - +
151A PRO* 3.3 6.1 - - - +
152A LEU* 2.7 56.5 + - + +
154A THR* 5.1 1.6 - - - +
157A PHE* 4.3 9.6 - - + -
158A CYS* 1.3 75.9 - - - +
160A THR* 1.3 62.9 + - - +
176A LEU* 4.3 19.3 - - + -
177A LYS 3.5 4.3 - - - +
178A VAL* 3.4 32.8 - - + -
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Residues in contact with THR 160 (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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151A PRO* 4.1 22.1 - - + +
158A CYS* 4.0 10.6 + - - -
159A ILE* 1.3 81.6 + - - +
161A LEU* 1.3 73.2 + - - +
162A ILE* 3.4 10.8 + - + -
176A LEU* 3.4 4.3 - - - -
177A LYS* 2.7 59.9 + - + +
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Residues in contact with LEU 161 (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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146A ALA* 3.8 23.5 - - + +
147A GLN* 3.6 22.5 + - + +
148A GLU* 3.3 35.0 - - + +
149A GLN 5.5 2.1 + - - -
151A PRO* 5.5 0.6 - - - +
160A THR* 1.3 79.9 - - - +
162A ILE* 1.3 61.8 + - - +
163A LYS* 3.7 26.9 - - - +
164A GLU* 4.1 25.6 - - + -
174A ARG* 4.1 13.0 - - + -
175A THR 4.0 1.8 - - - +
176A LEU* 3.9 16.4 - - + -
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Residues in contact with ILE 162 (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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160A THR* 3.4 8.7 + - + -
161A LEU* 1.3 77.9 - - - +
163A LYS* 1.3 77.3 + - + +
175A THR* 2.9 26.6 + - + +
176A LEU 4.3 2.0 - - - +
177A LYS* 3.7 44.2 - - + +
186A SER* 5.9 2.5 - - - +
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Residues in contact with LYS 163 (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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161A LEU* 3.6 7.8 - - - +
162A ILE* 1.3 90.2 - - + +
164A GLU* 1.3 65.4 + - - +
165A LYS* 5.8 10.1 - - + +
174A ARG* 3.7 0.5 - - - -
175A THR* 2.8 68.6 + - - +
188A TYR* 4.8 4.0 - - - -
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Residues in contact with GLU 164 (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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148A GLU* 5.3 4.3 + - - +
161A LEU* 4.1 21.7 - - + +
163A LYS* 1.3 80.4 - - - +
165A LYS* 1.3 67.1 - - - +
172A MET* 4.2 16.5 - - - +
173A LEU 3.3 11.0 - - - +
174A ARG* 3.5 33.7 + - + +
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Residues in contact with LYS 165 (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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163A LYS* 5.8 9.4 - - + +
164A GLU* 1.3 79.6 - - - +
166A TRP* 1.3 71.5 + - - +
167A LEU* 5.1 9.4 - - - +
172A MET* 3.3 10.5 - - - +
173A LEU* 2.7 67.6 + - + +
213A GLU* 5.1 2.0 + - - -
216A ARG* 5.9 1.2 - - - +
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Residues in contact with TRP 166 (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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165A LYS* 1.3 90.4 - - - +
167A LEU* 1.3 62.9 + - - +
168A ASN* 3.2 29.2 - - - +
169A GLU* 3.5 22.0 - - - -
171A ILE 3.3 27.4 - - - -
172A MET* 3.2 31.1 - - + +
193A MET* 3.9 24.0 - - + -
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Residues in contact with LEU 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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165A LYS* 3.7 12.2 + - - +
166A TRP* 1.3 73.9 - - - +
168A ASN* 1.3 78.6 + - + +
171A ILE* 2.9 29.6 + - + +
173A LEU* 4.6 11.6 - - + +
190A LEU* 4.7 5.4 - - + -
209A ALA* 4.2 21.3 - - + +
210A MET* 5.7 0.4 - - - -
213A GLU* 3.9 37.7 - - + +
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Residues in contact with ASN 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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166A TRP* 3.2 19.0 - - - +
167A LEU* 1.3 98.8 - - + +
169A GLU* 1.3 60.5 + - - +
170A ASP* 2.9 24.1 + - - +
171A ILE* 3.1 27.0 + - - +
206A HIS* 3.4 44.3 + - + +
209A ALA* 4.0 8.5 - - - +
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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