Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 4QKB
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 SER 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A SER 3.8 0.2 + - - -
140A PRO* 1.3 75.3 - - - +
142A VAL* 1.3 69.1 + - - +
143A MSE 4.3 0.4 - - - -
158A LEU* 4.0 3.1 - - - +
159A LEU* 3.0 36.6 + - - +
179A ILE* 3.5 23.7 - - - +
185A SER* 5.0 0.2 - - - -
192A ILE* 4.1 5.8 - - - -
194A ARG* 3.7 22.7 - - - +
197A ARG* 3.5 27.9 + - - -
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Residues in contact with VAL 142 (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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141A SER* 1.3 81.8 - - - +
143A MSE 1.3 70.3 + - - +
156A GLU* 4.1 16.8 - - + -
157A LEU 3.6 10.8 - - - +
158A LEU* 4.7 2.2 - - + -
178A GLU 3.5 0.5 - - - +
179A ILE* 3.4 6.4 - - - +
180A LEU* 3.0 55.5 + - + +
185A SER* 4.5 6.1 + - - +
186A PHE 4.0 9.2 - - - +
187A PHE* 3.8 19.3 - - + +
192A ILE* 3.8 29.6 - - + -
194A ARG* 5.3 0.4 - - - +
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Residues in contact with MSE 143 (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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142A VAL* 1.3 73.0 - - - +
144A ARG* 1.3 62.8 + - - +
145A LEU* 4.7 4.9 - - + -
156A GLU* 3.5 1.4 - - - -
157A LEU* 2.7 49.2 + - + +
159A LEU* 3.8 11.8 - - + +
165A TYR* 3.6 37.2 - - + +
167A LEU* 3.9 30.5 - - - -
177A HIS* 4.1 24.2 - - + -
178A GLU 3.1 12.1 - - - +
179A ILE* 3.7 24.1 - - + +
302A AKG 3.7 20.6 - - + +
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Residues in contact with ARG 144 (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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142A VAL 3.8 1.8 + - - -
143A MSE 1.3 74.0 - - - +
145A LEU* 1.3 62.3 + - - +
146A VAL* 3.9 18.8 + - + +
154A TRP* 4.6 12.3 - - + -
155A LEU 3.3 14.8 - - - +
156A GLU* 3.7 27.6 + - + -
176A SER 3.7 0.9 - - - +
177A HIS* 3.5 2.8 - - - -
178A GLU* 3.1 70.6 + - + +
180A LEU* 3.6 32.7 - - + +
184A GLU* 5.0 7.7 + - - +
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Residues in contact with LEU 145 (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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29A LEU* 5.0 2.7 - - + -
33A ALA* 3.9 28.0 - - + -
143A MSE 4.7 6.1 - - + -
144A ARG* 1.3 73.4 - - - +
146A VAL* 1.3 62.1 + - - +
154A TRP* 3.0 5.9 - - - +
155A LEU* 2.8 53.4 + - + +
157A LEU* 4.0 15.0 - - + -
167A LEU* 3.9 26.7 - - + -
171A ALA* 3.9 13.7 - - + +
175A PHE* 3.7 16.8 - - + -
176A SER 3.1 17.9 - - - +
177A HIS* 3.6 19.1 - - + -
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Residues in contact with VAL 146 (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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120A PRO* 6.1 0.9 - - + -
144A ARG* 3.9 26.0 - - + +
145A LEU* 1.3 76.4 - - - +
147A HIS* 1.3 74.3 + - - +
148A THR 3.4 0.2 + - - -
151A PRO* 3.8 35.2 - - + +
153A GLU 3.5 3.8 - - - +
154A TRP* 4.0 10.3 - - + -
175A PHE* 3.6 2.9 - - - -
176A SER* 2.9 38.1 + - - +
178A GLU* 4.0 12.1 - - - +
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Residues in contact with HIS 147 (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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146A VAL* 1.3 79.3 - - - +
148A THR* 1.3 68.9 + - - +
149A GLN* 3.1 38.2 + - + +
150A GLU* 3.2 39.8 + - + +
151A PRO* 3.9 1.9 - - - +
153A GLU* 2.7 40.1 + - + +
170A SER* 5.7 0.2 - - - -
174A ASP* 3.9 25.4 + - + +
175A PHE* 3.5 23.0 - + + -
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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