Contacts of the strand formed by residues 139 - 151 (chain A) in PDB entry 6D3N
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 GLY 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LYS 3.7 1.0 + - - -
138A ALA* 1.3 75.7 - - - +
140A VAL* 1.3 62.1 + - - -
141A TYR* 3.5 11.7 - - - -
205A HIS* 3.6 10.0 - - - -
206A LEU 2.7 39.2 + - - +
239A ARG* 3.8 11.4 - - - -
241A THR* 3.9 4.0 - - - -
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Residues in contact with VAL 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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139A GLY* 1.3 73.2 - - - -
141A TYR* 1.3 56.2 + - - +
203A LEU* 4.1 29.6 - - + -
204A LEU 3.2 14.4 - - - +
205A HIS* 4.4 17.3 - - + +
239A ARG* 3.6 2.9 - - - +
240A VAL* 2.8 37.4 + - + -
241A THR* 3.2 16.3 + - - +
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Residues in contact with TYR 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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91A MET* 4.2 11.7 - - + +
124A LEU* 4.6 12.2 - - + +
135A VAL* 3.7 17.6 - - + +
137A LYS* 2.9 33.8 + - - +
139A GLY 3.5 21.8 - - - -
140A VAL* 1.3 75.0 - - - +
142A TYR* 1.3 60.2 + - - +
143A VAL* 3.6 19.3 + - + +
203A LEU* 3.3 6.6 - - - -
204A LEU 2.7 34.4 + - - +
206A LEU* 3.7 18.2 - - + -
237A LEU* 3.9 19.1 - - + -
238A PHE 3.3 22.0 - - - +
239A ARG* 3.5 31.1 - - + -
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Residues in contact with TYR 142 (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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141A TYR* 1.3 71.2 - - - +
143A VAL* 1.3 58.9 + - - +
144A PHE* 3.8 23.1 - + + -
199A PHE* 4.4 12.0 - + - -
201A GLY* 3.6 20.4 + - - -
202A ARG* 3.8 24.9 - - - -
203A LEU* 4.1 13.0 - - + -
237A LEU* 3.1 6.1 - - - +
238A PHE* 2.9 70.3 + + + -
240A VAL* 4.0 12.1 - - + +
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Residues in contact with VAL 143 (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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141A TYR* 3.9 17.9 - - + +
142A TYR* 1.3 78.3 - - - +
144A PHE* 1.3 64.4 + - - +
165A LEU* 4.2 12.8 - - + -
179A LEU* 4.0 17.0 - - + +
201A GLY* 3.1 2.0 - - - -
202A ARG 2.9 35.5 + - - +
204A LEU* 3.9 22.9 - - + -
206A LEU* 4.5 3.6 - - + -
212A LEU* 5.3 3.1 - - + -
235A LEU* 3.9 20.4 - - + -
236A GLY 3.5 9.2 - - - +
237A LEU* 3.9 19.5 - - + -
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Residues in contact with PHE 144 (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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93A ALA 5.4 0.2 - - - -
94A GLN* 3.4 27.1 - - - -
142A TYR* 3.8 21.3 - + + -
143A VAL* 1.3 75.6 - - - +
145A PHE* 1.3 66.4 + - - +
146A GLN* 5.6 3.8 - - + -
179A LEU* 4.5 1.6 - - - -
199A PHE* 3.7 31.2 - + + -
200A GLN 3.2 11.9 - - - +
201A GLY* 4.0 4.5 - - - -
234A VAL* 4.7 8.1 - - + -
235A LEU* 3.5 5.5 - - - +
236A GLY* 2.9 60.0 + - - +
237A LEU* 3.8 3.4 - - - -
238A PHE* 4.0 22.2 - + - -
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Residues in contact with PHE 145 (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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109A TRP* 5.7 1.3 - + + -
144A PHE* 1.3 76.1 - - - +
146A GLN* 1.3 63.9 + - - +
163A LEU* 3.8 44.2 - - + -
164A ALA 4.4 0.9 - - - -
165A LEU* 4.1 21.1 - - + -
179A LEU* 3.6 36.3 - - + -
180A ALA* 3.9 8.7 - - - -
181A LEU* 3.7 27.4 - - + +
199A PHE* 3.5 6.0 - - - -
200A GLN* 3.0 40.7 + - + +
214A VAL* 4.4 10.3 - - + -
234A VAL 3.1 15.3 - - - +
235A LEU* 4.1 15.3 - - + -
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Residues in contact with GLN 146 (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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144A PHE* 5.6 3.7 - - + -
145A PHE* 1.3 78.3 - - - +
147A LEU* 1.3 61.2 + - - +
148A GLU* 5.9 0.6 + - - -
163A LEU* 4.4 2.4 - - - +
181A LEU* 4.7 0.9 - - - -
197A PHE* 3.4 36.0 - - + -
198A GLY 3.2 7.2 - - - -
199A PHE* 4.1 17.5 - - + +
232A ALA* 3.4 23.4 + - - +
233A THR* 3.3 9.2 - - - +
234A VAL* 3.1 45.7 + - + +
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Residues in contact with LEU 147 (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 GLN* 1.3 75.9 - - - +
148A GLU* 1.3 59.4 + - - +
149A LEU* 3.7 26.4 - - + +
161A VAL* 4.6 14.6 - - + +
163A LEU* 4.0 36.8 - - + +
181A LEU* 4.7 7.2 - - + +
183A VAL* 4.0 19.5 - - + -
196A ALA 4.0 0.2 - - - +
197A PHE* 3.3 8.7 - - - -
198A GLY 2.9 35.2 + - - +
216A LEU* 4.4 5.6 - - + -
228A LEU* 3.5 27.1 - - + -
232A ALA 4.2 0.4 - - - -
233A THR* 3.6 15.0 - - + +
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Residues in contact with GLU 148 (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 GLN* 5.9 0.5 + - - -
147A LEU* 1.3 74.2 - - - +
149A LEU* 1.3 72.1 + - - +
150A ARG* 5.6 0.7 - - - +
195A SER* 5.3 7.7 - - - -
196A ALA 3.4 9.2 - - - +
197A PHE* 4.1 18.0 - - + -
228A LEU* 3.5 12.1 - - - +
229A THR* 3.1 43.6 + - - +
232A ALA* 3.7 29.8 + - + +
233A THR* 4.1 3.8 + - - -
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Residues in contact with LEU 149 (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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102A LEU* 3.7 35.0 - - + -
147A LEU* 3.7 31.4 - - + -
148A GLU* 1.3 79.5 - - - +
150A ARG* 1.3 60.3 + - - +
161A VAL* 4.1 23.6 - - + -
183A VAL* 4.4 11.9 - - + -
185A LEU* 4.2 9.2 - - + -
195A SER* 3.3 9.2 - - - -
196A ALA* 2.8 35.9 + - + +
226A TRP* 4.0 20.2 - - + -
227A GLN 3.5 12.1 - - - +
228A LEU* 3.9 7.2 - - + -
229A THR* 3.9 3.6 + - - -
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Residues in contact with ARG 150 (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* 5.6 0.7 - - - +
149A LEU* 1.3 73.4 - - - +
151A ARG* 1.3 64.1 + - - +
152A VAL* 3.7 21.2 + - + +
194A ASN 3.6 4.9 - - - +
195A SER* 4.7 2.5 - - - +
226A TRP* 3.3 4.6 - - - -
227A GLN* 2.8 50.0 + - + +
228A LEU 4.7 2.7 - - - -
229A THR* 3.7 38.7 - - - +
230A GLN 5.3 1.4 - - - +
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Residues in contact with ARG 151 (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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150A ARG* 1.3 73.5 + - - +
152A VAL* 1.3 65.3 + - - +
153A VAL 3.7 13.3 + - - +
156A GLU* 4.2 17.0 - - - +
157A GLY 2.9 23.2 + - - +
186A PRO* 2.8 35.3 + - - +
187A PRO 3.9 7.5 + - - -
188A ALA* 4.1 19.0 - - - +
193A ARG 3.0 24.0 + - - +
194A ASN* 2.8 54.9 + - + +
225A ALA 3.8 7.9 - - - +
226A TRP* 3.3 29.9 - - + +
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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