Contacts of the strand formed by residues 141 - 151 (chain B) in PDB entry 3DIF
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 MET 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B SER* 1.3 82.3 - - - +
142B VAL* 1.3 59.6 + - - +
143B THR* 4.2 0.9 + - - -
188B THR* 3.8 28.7 - - + +
189B VAL 3.4 4.5 - - - +
190B PRO* 4.1 20.6 - - + -
191B SER* 4.5 1.3 - - - -
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Residues in contact with VAL 142 (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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132B PRO* 3.7 22.7 - - + -
141B MET* 1.3 73.4 - - - +
143B THR* 1.3 64.6 + - - +
144B LEU* 3.5 21.7 + - + -
187B VAL 3.7 0.7 - - - +
188B THR* 3.5 1.5 - - - -
189B VAL* 2.6 57.1 + - + +
190B PRO 4.0 7.4 - - - +
191B SER* 4.2 12.3 - - - +
194B TRP* 4.1 22.4 - - + +
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Residues in contact with THR 143 (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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114A THR* 4.9 11.6 - - - +
116A SER* 3.7 27.4 + - - +
118A PHE* 3.2 25.7 - - + -
135A PHE* 4.4 0.4 - - + -
137A ASN* 4.2 8.4 + - - +
132B PRO* 3.9 8.1 - - - +
141B MET 4.2 1.5 + - - -
142B VAL* 1.3 72.7 - - - +
144B LEU* 1.3 73.1 + - - +
186B SER* 4.2 16.6 - - - -
187B VAL 3.6 4.0 - - - +
188B THR* 2.8 26.3 + - - +
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Residues in contact with LEU 144 (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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118A PHE* 4.4 0.9 - - - -
130B LEU 3.9 5.2 - - - +
132B PRO* 4.4 3.1 - - + -
142B VAL* 3.5 34.3 - - + +
143B THR* 1.3 84.1 - - - +
145B GLY* 1.3 59.5 + - - +
160B TRP* 4.8 1.6 - - + -
186B SER* 3.2 5.5 - - - -
187B VAL* 2.7 49.1 + - + +
189B VAL* 4.9 4.0 - - + -
194B TRP* 3.6 34.5 - - + +
199B VAL* 3.8 22.4 - - + -
216B ILE* 3.6 30.3 - - + -
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Residues in contact with GLY 145 (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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118A PHE* 4.3 1.8 - - - -
135A PHE* 3.9 14.8 - - - -
130B LEU* 3.0 39.6 + - - +
144B LEU* 1.3 74.8 - - - +
146B CYS* 1.3 63.4 + - - +
160B TRP* 3.4 9.8 - - - -
185B SER 3.3 9.9 - - - -
216B ILE* 3.6 7.6 - - - +
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Residues in contact with CYS 146 (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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135A PHE* 4.9 0.2 - - - -
127B VAL* 3.6 23.8 - - - -
128B TYR 3.7 8.3 - - - -
130B LEU* 3.8 6.2 - - - +
145B GLY* 1.3 74.8 - - - +
147B LEU* 1.3 61.5 + - - +
148B VAL* 3.7 5.5 + - + +
160B TRP* 3.5 11.7 - - + -
184B SER* 3.3 5.6 - - - -
185B SER* 2.9 31.6 + - - +
201B CYS* 2.0 50.7 - - - -
203B VAL* 4.5 1.6 - - - -
214B LYS* 5.0 1.8 - - - -
216B ILE* 4.9 2.9 - - - -
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Residues in contact with LEU 147 (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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124A GLN* 3.9 19.1 - - - +
131A SER* 3.7 31.4 - - - +
133A VAL* 4.2 14.6 - - + -
178A THR* 5.1 4.9 - - + +
126B SER 3.4 2.3 - - - +
127B VAL* 3.2 5.4 - - - +
128B TYR* 2.8 57.6 + - + +
130B LEU* 3.8 16.5 - - + +
146B CYS* 1.3 70.0 - - - +
148B VAL* 1.3 62.5 + - - +
149B LYS* 4.4 8.7 - - + -
182B THR* 4.1 14.4 - - - +
183B LEU 3.9 4.5 - - - +
184B SER* 3.3 20.9 - - - +
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Residues in contact with VAL 148 (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 PRO* 3.6 27.1 - - + -
126B SER 3.6 2.2 - - - -
127B VAL* 4.2 6.1 - - + +
146B CYS* 4.2 10.1 - - + +
147B LEU* 1.3 74.6 - - - +
149B LYS* 1.3 58.9 + - - +
151B TYR* 3.9 15.5 - - + -
156B VAL* 4.2 6.3 - - + -
158B VAL* 4.4 5.8 - - + -
182B THR* 3.3 4.1 - - - -
183B LEU* 2.9 55.9 + - + +
185B SER 5.7 0.4 - - - +
203B VAL* 3.9 37.0 - - + -
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Residues in contact with LYS 149 (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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124A GLN* 3.9 13.5 - - - +
129A GLY* 6.4 0.9 - - - -
131A SER* 3.8 21.8 - - - +
160A LEU* 6.0 1.0 - - - +
178A THR* 6.2 0.2 - - - +
180A THR* 3.9 25.6 + - - +
125B PRO* 3.7 0.5 - - - +
126B SER* 2.8 47.0 + - - +
128B TYR* 4.4 12.3 - - + -
147B LEU* 4.4 11.4 - - + -
148B VAL* 1.3 74.3 - - - +
150B GLY* 1.3 69.2 + - - +
151B TYR* 3.6 2.5 - - - -
181B TYR 3.8 0.4 - - - -
182B THR* 3.8 28.7 + - - +
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Residues in contact with GLY 150 (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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123B THR* 3.3 15.4 - - - +
124B PRO 3.3 13.7 - - - +
149B LYS* 1.3 82.6 - - - +
151B TYR* 1.3 55.4 + - - -
180B LEU* 3.6 27.7 - - - +
181B TYR 2.9 14.0 + - - -
182B THR* 4.1 0.8 - - - -
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Residues in contact with TYR 151 (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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123B THR 3.3 13.2 - - - +
125B PRO* 3.6 26.9 - - + -
148B VAL* 3.9 22.4 - - + -
150B GLY* 1.3 78.1 - - - +
152B PHE* 1.3 61.2 + - - +
153B PRO 3.5 21.5 - - - -
154B GLU* 2.6 30.9 + - - -
156B VAL* 3.5 31.9 - - + +
174B ALA* 3.3 16.1 - - - +
180B LEU* 3.6 2.2 - - - -
181B TYR* 2.6 74.9 + + + +
182B THR* 4.2 2.0 - - - -
183B LEU* 3.6 12.3 - - + +
205B HIS* 3.8 2.9 - - - +
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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