Contacts of the strand formed by residues 153 - 164 (chain A) in PDB entry 3K3B
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 GLU 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLY 3.6 3.0 + - - +
152A THR* 1.3 68.9 - - - +
154A PHE* 1.3 61.1 + - - +
244A HIS 3.6 0.5 - - - +
245A MET* 3.4 1.6 - - - -
246A LYS* 2.7 65.3 + - + +
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Residues in contact with PHE 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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143A ILE 4.2 5.4 - - - -
144A PHE* 3.8 33.9 - + - -
147A LEU* 3.6 40.2 - - + -
148A THR* 3.6 35.4 - - - -
152A THR* 3.0 25.8 - - + +
153A GLU* 1.3 77.6 - - - +
155A SER* 1.3 60.8 + - - +
156A VAL* 3.9 18.2 - - + -
243A ILE* 4.2 1.6 - - + -
244A HIS 2.9 13.5 - - - +
245A MET* 4.2 4.0 - - + -
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Residues in contact with SER 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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154A PHE* 1.3 74.5 - - - +
156A VAL* 1.3 63.0 + - - +
157A LYS* 5.6 0.8 - - - +
203A THR* 5.4 8.3 - - - -
242A THR 3.5 1.7 - - - +
243A ILE* 3.5 5.6 - - - -
244A HIS* 3.0 45.8 + - - +
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Residues in contact with VAL 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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140A LEU* 4.5 5.2 - - + -
143A ILE* 3.7 29.2 - - + -
144A PHE* 3.8 20.4 - - + -
154A PHE* 3.9 13.0 - - + -
155A SER* 1.3 77.4 - - - +
157A LYS* 1.3 65.0 + - - +
158A VAL* 4.5 2.7 - - + -
203A THR* 3.5 8.4 - - - +
204A VAL* 2.8 54.4 + - + +
241A VAL* 3.8 24.2 - - + -
242A THR 3.6 2.2 - - - -
243A ILE* 4.3 4.7 - - + -
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Residues in contact with LYS 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 SER 5.6 0.9 - - - +
156A VAL* 1.3 75.8 - - - +
158A VAL* 1.3 62.0 + - - +
201A GLU* 3.6 42.7 + - + +
202A ILE 3.0 18.4 - - - +
203A THR* 4.2 8.5 - - + +
204A VAL 4.5 0.2 - - - +
240A SER 3.9 0.2 - - - +
241A VAL* 3.4 3.1 - - - +
242A THR* 2.8 58.6 + - - +
244A HIS* 4.2 23.6 - - + +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.0 13.5 - - + -
156A VAL* 4.5 0.2 - - + -
157A LYS* 1.3 80.1 - - - +
159A SER* 1.3 59.5 + - - +
172A LEU* 3.5 18.8 - - + +
201A GLU* 3.6 4.4 - - - -
202A ILE* 2.8 40.1 + - + +
204A VAL* 4.0 16.4 - - + -
213A ILE* 4.0 21.3 - - + -
239A PHE* 3.7 32.3 - - + -
240A SER 3.1 8.3 - - - +
241A VAL* 3.9 11.7 - - + -
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Residues in contact with SER 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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158A VAL* 1.3 74.2 - - - +
160A LEU* 1.3 61.8 + - - +
161A LEU 5.5 0.2 - - - -
172A LEU* 3.6 4.0 - - - -
199A LEU* 3.7 27.9 - - - +
200A GLU 3.3 20.6 - - - -
201A GLU* 4.1 12.2 + - - +
238A VAL 3.7 1.2 + - - +
239A PHE* 3.5 5.5 - - - -
240A SER* 2.9 48.5 + - - +
260A LYS* 5.2 0.7 + - - -
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Residues in contact with LEU 160 (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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136A ILE* 6.0 0.2 - - + -
159A SER* 1.3 76.8 - - - +
161A LEU* 1.3 63.3 + - - +
170A ASP* 3.6 7.0 + - - +
171A LEU* 2.9 52.7 + - + -
172A LEU* 3.4 29.1 + - + +
199A LEU* 4.7 1.6 - - - -
200A GLU 4.7 0.2 + - - -
217A GLY 4.2 6.1 - - - +
221A ARG* 3.6 11.0 - - - +
237A SER* 3.3 25.8 - - - +
238A VAL 3.4 17.5 - - - +
239A PHE* 3.9 18.8 - - + +
371A L31 3.3 25.6 - - + -
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Residues in contact with LEU 161 (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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159A SER* 4.3 0.4 - - - -
160A LEU* 1.3 76.4 - - - +
162A GLU* 1.3 63.2 + - - +
163A ILE* 3.8 27.1 - - + +
168A LEU* 4.9 6.7 - - + -
169A PHE 3.0 15.3 - - - +
171A LEU* 4.6 2.0 - - - -
182A LEU* 5.4 0.7 - - + -
196A ILE* 3.4 36.1 - - + -
199A LEU* 3.9 26.5 - - + -
237A SER* 3.7 2.1 - - - -
238A VAL* 2.8 56.0 + - + +
319A ILE* 4.3 13.9 - - + -
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Residues in contact with GLU 162 (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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161A LEU* 1.3 75.3 - - - +
163A ILE* 1.3 63.6 + - - +
164A TYR* 3.4 3.6 + - + +
167A GLU 3.4 2.8 - - - +
168A LEU* 3.9 0.2 - - - -
169A PHE* 2.9 40.5 + - + +
171A LEU* 3.4 31.1 - - + +
221A ARG* 3.0 40.9 + - - +
224A ALA* 5.0 7.1 - - - +
230A ALA* 4.5 12.8 - - - +
232A SER* 3.9 8.1 - - - -
235A SER* 3.3 25.5 + - - +
236A HIS 3.0 12.1 - - - +
237A SER* 4.2 2.0 - - - -
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Residues in contact with ILE 163 (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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161A LEU* 3.8 18.2 - - + -
162A GLU* 1.3 69.2 - - - +
164A TYR* 1.3 62.0 + - - +
165A ASN 4.2 0.4 - - - +
166A GLU* 4.2 10.8 - - - +
167A GLU 3.3 9.9 - - - +
168A LEU* 4.2 13.0 - - + -
234A ARG 4.6 0.2 - - - +
235A SER* 3.2 5.4 - - - -
236A HIS* 2.8 49.8 + - + -
238A VAL* 4.8 2.0 - - + -
315A LYS* 4.2 2.2 - - + -
316A LEU* 3.6 49.4 - - + +
319A ILE* 3.9 14.8 - - + -
372A NO3 3.2 26.2 - - - +
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Residues in contact with TYR 164 (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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162A GLU* 3.4 4.8 + - + +
163A ILE* 1.3 74.6 - - - +
165A ASN* 1.3 87.9 + - + +
166A GLU 3.2 0.2 - - - -
167A GLU* 3.0 31.6 + - - +
169A PHE* 3.9 20.1 - + + -
228A MET* 4.3 10.7 + - + -
229A ASN* 3.4 14.9 + - - +
230A ALA* 3.7 39.5 - - + -
231A TYR 4.3 3.4 - - - -
234A ARG* 3.5 43.3 + - + -
235A SER* 3.8 13.7 - - - +
288A ILE* 6.1 0.2 - - + -
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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