Contacts of the helix formed by residues 155 - 166 (chain A) in PDB entry 4BZ5
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 ASN 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.9 16.1 - - + -
63A HIS* 2.9 11.1 + - - +
140A TRP 3.5 12.9 + - - +
141A HIS* 3.3 22.4 + - - +
143A ALA* 2.8 30.3 + - + +
154A LEU* 1.3 71.1 - - - +
156A ASP* 1.3 60.7 + - - +
157A ILE* 3.2 13.9 + - - +
158A VAL* 3.0 33.9 + - + +
159A LEU* 3.2 27.2 + - - +
192A GLY 3.9 4.6 - - - -
193A VAL* 4.0 1.2 - - - +
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA* 3.5 28.0 - - + +
115A VAL* 3.8 16.8 - - + +
118A SER* 2.7 24.6 + - - +
119A LEU* 5.4 0.7 + - - +
138A GLY* 3.3 5.6 - - - -
139A GLY* 2.9 21.3 + - - -
140A TRP* 2.9 35.7 + - - +
154A LEU 3.1 5.6 + - - +
155A ASN* 1.3 72.7 - - - +
157A ILE* 1.3 59.4 + - - +
159A LEU* 3.9 2.9 - - - +
160A ALA* 2.9 30.5 + - - +
336A LEU* 4.1 3.3 - - - +
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Residues in contact with ILE 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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139A GLY* 3.6 25.6 - - - +
140A TRP 3.9 2.9 - - - +
141A HIS* 3.6 22.9 - - + -
155A ASN* 3.2 8.2 - - - +
156A ASP* 1.3 75.7 - - - +
158A VAL* 1.3 60.7 + - - +
160A ALA* 3.3 4.6 + - - +
161A ILE* 2.9 39.7 + - + +
182A TYR* 3.3 45.3 - - + +
193A VAL* 3.9 7.9 - - + -
279A VAL* 4.1 10.3 - - + -
281A GLN* 3.8 5.8 - - + -
336A LEU* 3.7 18.8 - - + -
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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
----------------------------------------------------------
62A PHE* 3.6 36.8 - - + -
155A ASN* 3.0 34.5 + - + +
157A ILE* 1.3 74.8 - - - +
159A LEU* 1.3 58.9 + - - +
161A ILE* 3.3 1.6 + - - +
162A HIS* 2.9 30.5 + - + +
192A GLY 4.2 0.4 - - - +
193A VAL* 3.9 15.5 - - + -
196A ALA* 3.6 27.6 - - + -
197A PHE* 3.9 18.8 - - + -
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Residues in contact with LEU 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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58A ALA 3.5 21.1 - - - +
59A VAL* 4.0 22.9 - - + +
61A ALA* 4.0 7.2 - - + -
62A PHE* 3.7 33.0 - - + +
63A HIS* 4.7 5.4 - - + -
115A VAL* 3.7 32.5 - - + -
119A LEU* 3.6 22.5 - - + +
155A ASN 3.2 17.5 + - - +
156A ASP* 3.9 4.7 - - - +
157A ILE 3.2 0.4 - - - -
158A VAL* 1.3 76.8 - - - +
160A ALA* 1.3 63.2 + - - +
162A HIS* 3.4 8.3 + - + +
163A ARG* 3.1 17.7 + - - +
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Residues in contact with ALA 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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118A SER* 3.7 27.1 - - - +
119A LEU* 3.9 9.7 - - - +
122A ALA* 4.0 3.6 - - + +
156A ASP 2.9 19.2 + - - +
157A ILE* 3.7 5.4 - - + +
159A LEU* 1.3 77.7 - - - +
161A ILE* 1.3 62.6 + - + +
163A ARG* 3.1 5.7 + - - +
164A LEU* 3.0 26.8 + - - +
279A VAL* 6.0 0.2 - - + -
334A LEU* 4.0 20.9 - - + -
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Residues in contact with ILE 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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157A ILE* 2.9 37.5 + - + +
160A ALA* 1.3 72.1 - - + +
162A HIS* 1.3 61.4 + - - +
164A LEU* 3.1 7.4 + - - +
165A VAL* 2.9 31.7 + - + +
180A VAL* 4.2 8.5 - - + -
182A TYR* 4.1 19.7 - - + -
193A VAL* 4.1 10.8 - - + -
197A PHE* 3.4 35.9 - - + -
203A VAL* 3.7 26.2 - - + -
279A VAL* 3.9 21.8 - - + -
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Residues in contact with HIS 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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61A ALA* 4.1 31.9 + - + +
62A PHE* 6.6 0.2 - - + -
158A VAL* 2.9 19.6 + - + +
159A LEU* 3.5 11.4 + - + +
160A ALA 3.3 0.2 - - - -
161A ILE* 1.3 77.3 - - - +
163A ARG* 1.3 63.5 + - - +
165A VAL* 3.1 10.7 - - + +
166A SER* 2.9 51.7 + - - -
197A PHE* 4.3 8.4 - + + -
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Residues in contact with ARG 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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47A LEU* 3.7 32.7 - - - +
49A TRP* 5.5 2.2 - - - +
58A ALA* 6.0 1.6 - - - +
119A LEU* 3.7 32.4 + - + +
122A ALA* 4.0 7.9 - - + -
123A SER* 2.6 37.8 + - - +
126A ILE* 3.7 13.7 - - + -
159A LEU 3.1 12.7 + - - +
160A ALA 3.1 9.6 + - - +
162A HIS* 1.3 79.8 + - - +
164A LEU* 1.3 61.6 + - - +
166A SER* 3.5 5.3 + - - -
167A SER* 3.3 21.5 + - - -
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Residues in contact with LEU 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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122A ALA* 3.8 23.3 - - + +
125A LEU* 4.7 7.2 - - + -
126A ILE* 3.8 23.6 - - + -
160A ALA 3.0 20.1 + - - +
161A ILE* 3.6 10.3 - - - +
163A ARG* 1.3 76.6 - - - +
165A VAL* 1.3 58.9 + - - +
167A SER* 2.6 25.7 + - - -
178A THR* 3.6 10.0 - - - +
180A VAL* 4.2 7.2 - - + -
277A TYR* 3.9 39.7 - - + -
279A VAL* 3.6 30.7 - - + -
334A LEU* 4.9 4.5 - - + -
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Residues in contact with VAL 165 (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 ILE* 2.9 17.6 + - + +
162A HIS* 3.1 26.2 - - + +
164A LEU* 1.3 76.7 - - - +
166A SER* 1.3 63.7 + - - +
167A SER 3.2 1.3 + - - -
178A THR* 3.9 25.8 + - + +
180A VAL* 3.3 29.2 - - + +
197A PHE* 5.3 3.8 - - + -
202A ARG* 4.9 7.2 - - + +
203A VAL* 3.4 24.7 - - + -
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Residues in contact with SER 166 (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 HIS* 2.9 41.4 + - - -
163A ARG* 3.8 5.6 - - - -
164A LEU 3.2 0.2 - - - -
165A VAL* 1.3 78.4 - - - +
167A SER* 1.3 60.5 + - - +
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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