Contacts of the strand formed by residues 154 - 165 (chain A) in PDB entry 4GEK
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ALA* 3.3 15.9 - - + +
127A SER 3.9 3.4 - - - -
128A MET 3.8 12.1 - - - +
129A VAL* 3.9 17.0 - - + -
150A ILE* 3.0 24.5 + - + +
151A TYR* 3.7 6.5 - - - +
152A GLN 3.4 2.2 - - - +
153A GLY* 1.3 81.0 - - - +
155A ASN* 1.3 62.5 + - - +
156A PRO* 4.4 0.3 - - - +
158A GLY* 4.2 3.6 - - - +
159A ALA 3.8 35.0 - - - +
223A PHE* 3.6 33.9 - - + -
242A LYS* 2.8 34.7 + - + -
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Residues in contact with ASN 155 (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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55A GLN* 6.0 0.6 - - - +
58A THR* 3.7 18.8 - - - +
125A ASN* 3.0 43.4 + - - +
126A ALA 2.8 18.5 + - - +
127A SER* 4.4 4.3 - - - +
153A GLY 4.3 1.0 - - - +
154A LEU* 1.3 76.3 - - - +
156A PRO* 1.3 83.0 - - + +
157A GLY 3.3 0.2 + - - -
158A GLY* 2.9 17.3 + - - +
242A LYS* 3.8 5.7 - - - +
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Residues in contact with PRO 156 (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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55A GLN* 6.1 0.5 - - - +
154A LEU 4.4 1.8 - - - +
155A ASN* 1.3 95.3 - - + +
157A GLY* 1.3 59.7 + - - +
158A GLY 3.4 0.3 + - - -
242A LYS* 4.2 10.0 - - + +
243A ALA 3.4 11.2 - - - +
244A GLU* 3.5 25.5 - - - +
246A ALA* 3.8 21.1 - - + +
247A ALA* 5.4 2.2 - - - +
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Residues in contact with GLY 157 (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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53A PHE* 3.4 26.2 - - - +
55A GLN* 5.7 3.7 + - - -
156A PRO* 1.3 72.7 - - - +
158A GLY* 1.3 65.1 + - - +
241A LEU* 6.0 0.2 - - - -
242A LYS 2.9 19.9 + - - -
243A ALA 3.3 4.9 + - - -
244A GLU* 3.8 21.5 - - - -
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Residues in contact with GLY 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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53A PHE* 4.5 0.9 - - - -
127A SER* 3.2 22.0 - - - -
154A LEU* 4.2 12.4 - - - +
155A ASN* 2.9 17.9 + - - -
156A PRO 3.2 1.0 + - - -
157A GLY* 1.3 80.7 - - - +
159A ALA* 1.3 59.5 + - - -
241A LEU* 3.6 3.1 - - - +
242A LYS* 2.9 27.0 + - - +
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Residues in contact with ALA 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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49A LEU* 4.0 22.4 - - + -
53A PHE* 3.8 17.5 - - + -
127A SER 3.0 8.0 + - - +
128A MET* 3.1 9.2 - - + +
129A VAL 2.9 24.8 + - - +
154A LEU* 3.8 7.7 - - - +
158A GLY* 1.3 75.0 - - - +
160A LEU* 1.3 58.2 + - - +
161A VAL 4.3 0.2 - - - -
239A VAL* 4.7 1.1 - - + -
240A ALA 3.4 4.9 - - - +
241A LEU* 3.8 22.0 - - + -
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Residues in contact with LEU 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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129A VAL* 3.2 34.1 - - + +
131A LEU* 4.2 15.3 - - + +
147A LEU* 3.9 17.7 - - + -
150A ILE* 4.2 9.9 - - + -
154A LEU* 4.4 0.8 - - + +
159A ALA* 1.3 75.1 - - - +
161A VAL* 1.4 79.2 + - - +
162A LEU* 4.4 6.3 - - + +
218A LEU* 3.7 29.6 - - + -
223A PHE* 3.9 26.7 - - + -
238A LEU 3.8 0.5 - - - +
239A VAL* 3.4 5.7 - - - +
240A ALA* 2.9 35.2 + - + +
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Residues in contact with VAL 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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42A ILE* 5.1 0.4 - - + -
46A ILE* 4.0 24.5 - - + -
49A LEU* 3.5 31.6 - - + -
128A MET* 4.3 13.7 - - + -
129A VAL 2.9 10.0 + - - +
130A VAL* 4.6 6.5 - - + -
131A LEU 2.8 32.4 + - - +
132A ASN* 4.9 0.2 - - - +
160A LEU* 1.4 78.9 - - - +
162A LEU* 1.3 55.8 + - - +
163A SER* 3.8 9.2 - - - +
229A TRP* 3.9 16.8 - - + -
237A SER* 3.3 24.9 - - - +
238A LEU 3.5 4.0 - - - +
239A VAL* 4.8 1.3 - - + -
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Residues in contact with LEU 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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131A LEU* 3.6 24.7 - - + +
135A LEU* 3.8 32.1 - - + -
147A LEU* 4.7 5.8 - - + -
160A LEU* 4.1 12.1 - - + -
161A VAL* 1.3 72.9 - - - +
163A SER* 1.3 59.7 + - - +
164A GLU* 4.0 13.0 - - + +
214A HIS* 3.9 25.8 - - + +
218A LEU* 4.2 30.5 - - + -
237A SER* 3.3 0.9 - - - -
238A LEU* 2.7 49.8 + - + +
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Residues in contact with SER 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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42A ILE* 3.5 4.3 - - - +
131A LEU 2.9 8.9 + - - +
132A ASN* 2.7 31.3 + - - -
133A PHE* 2.8 44.2 + - - -
161A VAL* 3.8 5.2 - - - +
162A LEU* 1.3 70.3 - - - +
164A GLU* 1.3 67.3 + - - +
236A GLY 3.2 12.6 - - - -
237A SER* 2.7 21.8 + - - -
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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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133A PHE* 3.5 9.7 - - - -
134A THR 3.8 0.5 + - - -
135A LEU* 3.3 17.7 + - - +
136A GLN* 2.9 51.5 + - - +
143A ARG* 5.5 0.5 - - - -
162A LEU* 4.0 14.6 + - + +
163A SER* 1.3 83.6 - - - +
165A LYS* 1.3 69.5 + - - +
166A PHE* 3.7 10.9 + - + -
208A THR* 5.4 0.9 - - - -
209A ASP* 4.9 4.3 + - - +
214A HIS* 3.5 38.0 + - + +
235A PHE* 3.6 0.5 - - - -
236A GLY 2.9 32.1 + - - +
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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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133A PHE* 3.9 3.0 - - - -
136A GLN* 2.9 17.3 + - - +
164A GLU* 1.3 81.9 - - - +
166A PHE* 1.3 65.1 + - - +
178A PHE* 4.7 14.4 - - - -
181A HIS* 4.2 6.5 + - - -
203A GLU* 2.8 38.3 + - - +
206A MET* 3.8 20.2 - - + -
208A THR* 3.3 28.6 - - + +
209A ASP 4.3 1.9 + - - +
234A ASN* 3.5 34.2 - - - +
235A PHE* 3.6 31.9 - - + -
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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