Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 1SOT
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 VAL 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TYR* 3.8 38.4 - - + +
152A GLY 3.4 0.2 + - - -
153A ASP* 1.3 74.6 - - - +
155A VAL* 1.3 68.8 + - - +
156A LEU* 4.9 2.7 - - + -
170A GLN* 4.1 10.1 - - - +
171A GLY 3.5 10.3 - - - +
172A ILE* 4.2 4.0 - - + -
207A ASN* 3.5 22.3 - - - +
208A SER* 3.9 7.0 + - - +
45C ALA* 3.1 36.2 + - + +
46C SER 4.3 0.7 - - - +
47C TYR* 3.8 30.1 - - + -
170C GLN* 5.9 0.2 - - - +
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Residues in contact with VAL 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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153A ASP 4.1 3.8 - - - +
154A VAL* 1.3 78.0 - - - +
156A LEU* 1.3 61.5 + - - +
170A GLN* 3.2 8.1 - - - +
171A GLY 2.9 34.6 + - - +
172A ILE 4.4 1.3 - - - -
173A ILE* 3.8 20.0 - - + -
192A THR* 3.5 22.2 - - - +
194A ALA* 4.4 3.1 - - + -
205A LEU* 3.0 42.8 - - + -
206A VAL 3.2 14.4 - - - +
207A ASN 5.0 0.2 - - - -
213A MSE 3.9 15.3 - - + -
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Residues in contact with LEU 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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47A TYR* 3.9 27.8 - - + -
50A ALA* 3.7 28.5 - - + -
51A VAL* 3.8 25.4 - - + +
154A VAL* 4.9 3.4 - - + -
155A VAL* 1.3 77.7 - - - +
157A ALA* 1.3 59.9 + - - +
158A ILE* 4.0 2.2 + - + -
168A ILE* 3.9 11.2 - - + -
169A THR 3.3 5.4 - - - +
170A GLN* 3.3 29.4 - - + -
204A ALA 3.5 1.6 - - - +
205A LEU* 3.2 5.8 - - - -
206A VAL* 2.8 46.3 + - + +
207A ASN 5.0 2.7 - - - +
208A SER* 5.7 0.4 - - - -
152B GLY* 5.5 0.2 - - - -
172B ILE* 4.3 8.5 - - + -
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Residues in contact with ALA 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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155A VAL 4.2 0.2 - - - -
156A LEU* 1.3 72.3 - - - +
158A ILE* 1.3 60.2 + - - +
159A GLY 4.0 0.6 + - - -
167A THR 3.6 1.0 - - - +
168A ILE* 3.2 7.3 - - - +
169A THR* 2.9 43.6 + - - +
194A ALA* 4.1 5.1 - - + +
196A ILE* 3.6 31.0 - - + -
200A ASN* 3.8 9.5 - - - +
204A ALA 3.3 5.2 - - - -
205A LEU* 3.9 8.5 - - + +
216A ASN* 4.0 3.4 - - - +
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Residues in contact with ILE 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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50A ALA 5.2 2.0 - - - +
51A VAL* 5.2 3.4 - - - -
54A ALA* 4.1 20.0 - - + -
55A ALA* 4.2 12.6 - - + +
58A VAL* 3.6 32.3 - - + +
156A LEU* 4.4 5.4 - - + +
157A ALA* 1.3 78.5 - - - +
159A GLY* 1.3 61.0 + - - +
166A GLN* 3.9 15.3 - - - -
167A THR 3.4 2.5 - - - -
168A ILE* 3.8 30.3 - - + -
200A ASN* 3.6 2.6 - - - +
203A GLY* 3.4 6.6 - - - -
204A ALA* 2.7 34.1 + - + +
206A VAL* 4.0 26.2 - - + -
216A ASN* 4.1 1.1 + - - +
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Residues in contact with GLY 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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81A SER* 3.7 5.8 - - - -
158A ILE* 1.3 75.1 - - - +
160A ASN* 1.3 61.0 + - - -
161A PRO* 2.9 3.7 - - - +
167A THR 2.6 41.9 + - - +
199A GLY 3.1 20.2 - - - -
200A ASN* 3.1 15.0 + - - -
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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