Contacts of the strand formed by residues 109 - 121 (chain B) in PDB entry 1SMV
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 LYS 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A TYR* 3.9 26.9 + - + +
191A GLU 3.0 24.5 + - - -
192A LEU* 3.7 4.6 - - - +
193A GLY* 3.6 17.6 - - - +
221A PRO 4.8 2.4 + - - -
107B TRP* 4.4 2.2 - - - +
108B SER* 1.3 87.6 - - - +
110B TYR* 1.3 63.6 + - - +
196B TRP* 4.0 15.9 - - + +
197B TYR 3.2 18.8 - - - +
198B PRO* 4.2 8.7 - - + -
199B TYR* 4.4 1.6 - - - +
250B MET* 3.6 2.9 - - - +
251B ILE* 3.0 43.6 + - + +
252B GLU* 2.8 28.0 + - - +
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Residues in contact with TYR 110 (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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92B MET* 3.5 15.1 - - - +
93B PRO* 3.3 41.0 - - + +
104B ALA* 6.1 1.6 - - + -
109B LYS* 1.3 76.5 - - - +
111B SER* 1.3 68.7 + - - +
112B TRP* 3.8 24.7 - + - -
195B LYS 3.4 0.2 - - - +
196B TRP* 3.2 9.7 - - - -
197B TYR* 2.8 61.1 + + + +
198B PRO 3.4 23.9 + - - -
199B TYR* 4.0 11.7 - + + -
200B LYS 5.3 0.2 - - - -
219B LEU 4.3 2.9 + - - -
221B PRO* 3.9 8.3 - - - +
248B ILE* 4.0 20.0 - - + -
249B GLN 3.1 13.9 - - - +
250B MET* 4.7 4.5 - - + -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 1.3 80.5 - - - +
112B TRP* 1.3 70.3 + - - +
113B LEU* 3.5 1.0 + - - +
195B LYS* 3.1 46.6 + - - +
196B TRP* 3.6 20.9 - - - -
197B TYR* 5.8 0.2 - - - -
248B ILE* 3.6 2.8 - - - +
249B GLN* 3.0 38.2 + - - +
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Residues in contact with TRP 112 (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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91B VAL* 3.0 28.3 + - + +
92B MET* 3.9 2.9 - - - -
93B PRO* 3.8 22.7 - - + -
96B VAL* 4.0 18.2 - - + -
100B LEU* 3.8 20.9 - - + -
110B TYR* 3.8 15.9 - + - -
111B SER* 1.3 78.1 + - - +
113B LEU* 1.3 64.1 + - - +
115B VAL* 3.3 24.9 - - + -
187B LEU* 4.3 9.0 - - + -
189B VAL* 3.6 28.0 - - + +
192B LEU* 4.7 6.9 - - + +
195B LYS 4.4 1.6 + - - -
197B TYR* 5.7 2.6 - + - -
221B PRO* 3.8 19.2 - - + +
246B TYR* 3.8 22.9 - + + -
247B THR 4.2 4.5 - - - -
248B ILE* 3.7 28.3 - - + -
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Residues in contact with LEU 113 (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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68B THR* 5.0 4.5 - - + -
111B SER 3.5 1.0 + - - -
112B TRP* 1.3 78.2 - - - +
114B SER* 1.3 63.6 + - - +
189B VAL* 3.8 17.5 - - - +
195B LYS* 4.3 10.3 - - - +
247B THR* 2.9 36.1 + - + +
249B GLN* 3.7 44.9 - - + +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TRP 3.5 0.8 - - - -
113B LEU* 1.3 82.5 - - - +
115B VAL* 1.3 71.0 + - - +
116B ARG* 4.9 2.9 + - - +
186B THR* 5.8 1.6 - - - +
187B LEU 5.7 0.4 - - - -
189B VAL* 4.4 4.9 - - - -
245B THR 4.6 4.3 + - - -
246B TYR* 3.1 5.5 - - - +
247B THR* 2.9 43.8 + - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 4.0 11.7 - - + -
96B VAL* 5.4 1.1 - - + -
112B TRP* 3.3 49.4 - - + -
114B SER* 1.3 82.2 + - - +
116B ARG* 1.3 63.2 + - - +
117B TYR* 3.6 19.9 - - + -
186B THR* 3.3 5.2 - - - -
187B LEU* 2.9 43.3 + - + +
189B VAL* 4.7 3.6 - - + +
244B ASP* 3.6 23.1 - - - +
245B THR 3.8 2.9 - - - -
246B TYR* 4.5 2.0 - - + +
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Residues in contact with ARG 116 (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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114B SER* 5.3 3.4 - - - +
115B VAL* 1.3 74.0 - - - +
117B TYR* 1.3 63.0 + - - +
118B THR* 3.4 15.9 - - - +
170B PHE* 3.6 48.3 - - - -
184B SER* 2.8 25.1 + - - +
185B THR* 3.4 5.4 - - - +
186B THR* 3.3 35.5 + - + +
243B TYR 3.9 0.2 - - - +
244B ASP* 3.5 2.4 - - - -
245B THR* 2.8 50.9 + - - +
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Residues in contact with TYR 117 (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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75B THR* 4.1 7.4 - - + -
89B GLU* 3.0 36.6 + - - +
91B VAL* 3.5 25.9 - - + +
96B VAL* 3.6 5.7 - - - +
115B VAL* 3.6 15.9 - - + -
116B ARG* 1.3 71.0 - - - +
118B THR* 1.3 61.6 + - - +
133B MET* 4.3 14.6 - - - +
135B PHE* 4.1 21.8 - + - -
183B ILE 4.1 0.3 - - - +
184B SER* 3.2 2.8 + - - -
185B THR* 2.9 37.6 + - + +
224B LEU* 4.1 30.5 - - + -
242B ILE* 4.0 23.8 - - + -
243B TYR 3.6 2.7 - - - -
244B ASP* 3.2 24.9 - - - -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 3.4 15.6 + - - +
117B TYR* 1.3 73.2 - - - +
119B TYR* 1.3 71.8 + - - +
120B ILE* 3.9 4.6 + - + +
133B MET* 5.4 0.2 - - - -
167B GLY* 3.8 32.8 - - - +
170B PHE* 4.0 7.6 - - + +
171B ILE* 5.0 8.3 - - + -
182B ALA* 5.1 0.4 - - + -
183B ILE 3.6 4.5 - - - +
184B SER* 2.9 28.9 + - - -
241B ARG 3.8 0.3 - - - +
242B ILE* 3.5 3.5 - - - +
243B TYR* 2.9 37.7 + - - +
245B THR* 4.6 2.1 + - - -
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Residues in contact with TYR 119 (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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78B ILE* 4.1 11.7 - - + -
118B THR* 1.3 77.2 - - - +
120B ILE* 1.3 65.9 + - - +
121B PRO* 3.9 7.2 - - - +
131B ILE* 3.6 28.7 - - + -
133B MET* 4.8 3.9 - - + +
161B VAL* 2.7 41.1 + - + +
163B SER 3.9 14.6 - - - -
164B GLY* 3.9 12.0 - - - +
183B ILE* 2.9 45.3 + - + +
239B ALA* 3.2 23.1 - - - +
240B GLY* 3.7 25.6 - - - -
241B ARG 3.4 17.9 - - - -
242B ILE* 4.2 8.3 - - + +
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Residues in contact with ILE 120 (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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118B THR* 4.4 3.6 - - + +
119B TYR* 1.3 84.6 - - - +
121B PRO* 1.3 79.3 - - + +
122B SER* 5.2 0.2 - - - -
164B GLY 4.1 7.0 - - - +
165B SER* 4.5 3.6 - - - +
167B GLY* 3.8 7.6 - - - -
168B LEU* 3.6 41.7 - - + +
171B ILE* 3.4 27.1 - - + -
240B GLY* 3.4 0.7 - - - -
241B ARG* 2.8 30.6 + - - +
243B TYR* 3.8 18.6 - - + +
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Residues in contact with PRO 121 (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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119B TYR* 3.9 5.6 - - + +
120B ILE* 1.3 101.6 - - + +
122B SER* 1.3 61.2 + - - +
123B CYS 4.7 2.7 - - - +
161B VAL 3.5 15.7 - - - +
162B TRP* 3.5 26.2 - - - +
163B SER 3.4 22.0 - - - +
164B GLY 4.0 1.3 - - - -
165B SER* 4.0 24.7 - - - +
239B ALA 3.8 5.6 - - - +
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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