Contacts of the strand formed by residues 151 - 157 (chain A) in PDB entry 3SCG
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 ILE 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A VAL* 3.6 21.8 - - + -
146A VAL* 4.1 11.6 - - + +
148A GLU 4.9 1.1 - - - +
149A GLY 4.2 0.6 + - - -
150A GLU* 1.3 73.2 - - - +
152A HIS* 1.3 61.9 + - - +
153A MET* 3.9 9.4 - - + +
165A LEU* 3.4 6.2 - - - +
166A LEU* 2.7 73.8 + - + +
172A MET* 4.7 1.3 - - + -
182A PHE* 4.2 15.5 - - + -
183A THR 3.9 6.3 - - - +
191A ALA* 3.2 31.6 - - + -
192A LYS 4.2 5.4 - - - +
193A LEU* 3.6 24.2 - - + -
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Residues in contact with HIS 152 (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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129A PRO* 3.3 30.4 - - + +
150A GLU 4.0 0.2 + - - -
151A ILE* 1.3 73.1 - - - +
153A MET* 1.3 59.9 + - - +
154A LYS* 3.3 25.6 + - + +
163A GLU* 2.8 37.2 + - + +
164A ALA 3.6 13.0 - - - -
165A LEU* 4.1 20.6 - - + -
181A ALA 4.1 0.3 - - - +
182A PHE* 3.8 3.4 - - - -
183A THR* 2.9 39.5 + - - +
184A ALA 4.1 6.7 - - - +
185A ALA* 4.4 1.6 - - - -
186A LYS 5.7 0.2 - - - -
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Residues in contact with MET 153 (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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151A ILE* 3.7 0.8 - - - +
152A HIS* 1.3 74.7 - - - +
154A LYS* 1.3 69.3 + - - +
155A TRP* 3.8 37.0 - - + -
163A GLU* 3.4 6.6 - - - +
164A ALA* 2.9 36.8 + - - +
166A LEU* 3.7 22.9 - - + -
172A MET* 4.2 17.0 - - + -
173A PHE 5.5 0.7 - - - +
174A VAL* 3.5 32.3 - - + -
180A HIS* 4.7 2.9 - - + -
181A ALA 3.6 4.9 - - - -
182A PHE* 3.4 35.4 - - + -
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Residues in contact with LYS 154 (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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129A PRO* 2.8 32.3 + - - +
130A ASP* 4.0 5.7 + - - +
132A ALA* 4.0 17.7 - - + +
134A PHE* 3.7 19.9 - - + -
152A HIS* 3.3 31.4 - - + +
153A MET* 1.3 81.3 - - - +
155A TRP* 1.3 62.2 + - - +
161A PRO* 4.2 12.6 - - + +
162A LYS 3.5 6.3 - - - +
163A GLU* 3.6 25.1 + - + -
180A HIS* 3.0 5.0 - - - +
181A ALA* 2.6 42.7 + - + +
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Residues in contact with TRP 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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134A PHE* 3.9 5.4 - - - -
153A MET* 3.8 33.4 - - + -
154A LYS* 1.3 75.0 - - - +
156A GLY* 1.3 65.9 + - - +
161A PRO* 3.4 3.8 - - - +
162A LYS* 3.0 72.4 + - + +
163A GLU 3.8 28.3 - - - -
164A ALA* 3.9 13.5 - - + -
174A VAL* 5.7 1.6 - - + -
178A VAL* 4.4 15.0 - - + -
179A PRO 3.2 13.5 - - - +
180A HIS* 4.0 8.1 - - + -
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Residues in contact with GLY 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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134A PHE* 3.8 2.5 - - - -
155A TRP* 1.3 81.3 - - - +
157A ASP* 1.3 64.5 + - - -
158A LYS 3.3 3.8 + - - -
161A PRO* 5.0 0.2 - - - -
162A LYS* 5.6 2.9 - - - -
178A VAL* 4.4 3.5 - - - +
179A PRO* 2.8 44.6 + - - +
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Residues in contact with ASP 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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134A PHE* 4.5 0.2 - - - -
155A TRP 4.1 1.0 + - - -
156A GLY* 1.3 69.1 - - - -
158A LYS* 1.3 55.9 + - - +
159A GLU* 3.5 18.3 + - - +
160A ASN* 2.6 58.2 + - + +
161A PRO* 2.8 18.2 - - - -
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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