Contacts of the strand formed by residues 154 - 159 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ALA* 2.9 38.8 + - + +
47B TYR* 3.8 30.3 - - + -
47C TYR* 3.7 37.0 - - + +
152C GLY 3.5 0.2 + - - -
153C ASP* 1.3 72.5 - - - +
155C VAL* 1.3 68.7 + - - +
156C LEU* 5.0 1.3 - - + -
170C GLN* 3.9 15.9 - - + +
171C GLY 3.5 10.5 - - - +
172C ILE* 4.2 4.0 - - + +
207C ASN* 3.4 19.4 - - - +
208C SER* 3.7 6.7 + - - +
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Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ASP 4.1 0.2 - - - +
154C VAL* 1.3 80.3 - - - +
156C LEU* 1.3 65.8 + - - +
170C GLN* 3.5 3.6 - - - +
171C GLY 2.9 31.4 + - - +
172C ILE 3.8 13.7 - - - -
173C ILE* 3.7 24.5 - - + +
192C THR* 3.4 25.4 - - - +
194C ALA* 4.2 2.0 - - + +
205C LEU* 4.0 24.0 - - + -
206C VAL 3.1 13.0 - - - +
207C ASN* 4.4 0.7 - - - +
213C MSE 4.1 20.2 - - + -
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Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 4.0 8.7 - - + -
47C TYR* 3.8 31.9 - - + +
50C ALA* 3.8 17.3 - - + -
51C VAL* 3.7 30.7 - - + +
154C VAL* 5.0 1.3 - - + -
155C VAL* 1.3 74.6 - - - +
157C ALA* 1.3 60.3 + - - +
158C ILE* 3.7 3.8 + - + +
168C ILE* 3.9 11.2 - - + -
169C THR 3.2 8.5 - - - +
170C GLN* 3.7 33.7 - - + -
204C ALA 3.5 1.0 - - - +
205C LEU* 3.3 7.2 - - - -
206C VAL* 2.8 45.2 + - + +
207C ASN 5.1 2.2 - - - +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL 4.2 0.2 - - - -
156C LEU* 1.3 72.9 - - - +
158C ILE* 1.3 60.1 + - - +
159C GLY 4.0 0.7 - - - -
167C THR 3.5 2.3 - - - +
168C ILE* 3.3 5.7 - - - +
169C THR* 2.7 49.9 + - - +
194C ALA* 4.1 6.4 - - + +
195C SER 3.9 1.6 - - - +
196C ILE* 3.9 19.5 - - + -
200C ASN* 3.8 18.4 - - - +
204C ALA 3.5 4.9 - - - -
205C LEU* 3.8 9.0 - - + -
216C ASN* 4.2 1.8 - - - +
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Residues in contact with ILE 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA 5.1 2.7 - - - +
51C VAL* 5.2 2.5 - - - -
54C ALA* 3.9 28.5 - - + -
55C ALA* 4.0 12.1 - - + +
58C VAL* 3.6 25.3 - - + +
156C LEU* 4.3 6.5 - - + +
157C ALA* 1.3 74.8 - - - +
159C GLY* 1.3 60.8 + - - +
160C ASN* 3.9 1.8 - - - +
166C GLN* 3.8 20.0 - - + +
167C THR 3.7 2.5 - - - -
168C ILE* 3.6 33.2 - - + -
200C ASN* 3.6 2.0 - - - -
203C GLY* 3.5 4.7 - - - -
204C ALA* 2.7 35.5 + - + +
206C VAL* 4.1 16.8 - - + -
216C ASN* 4.2 0.6 + - - -
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Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C SER* 3.7 3.6 - - - -
158C ILE* 1.3 75.5 - - - +
160C ASN* 1.3 61.3 + - - -
161C PRO* 2.8 3.8 - - - +
167C THR* 2.8 36.2 + - - +
199C GLY 2.9 19.5 - - - -
200C ASN* 2.9 22.0 + - - -
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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