Contacts of the helix formed by residues 148 - 165 (chain P) in PDB entry 5A31
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 148 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476J PRO* 3.3 44.1 - - - +
477J GLN* 3.5 28.2 + - + +
147P LYS* 1.3 80.8 - - + +
149P GLU* 1.3 63.6 - - - +
150P ALA* 3.1 5.2 + - - -
151P LEU* 3.3 17.0 + - - +
152P ARG* 3.5 22.5 + - - +
181P LYS 5.1 0.7 - - - +
182P LEU* 3.3 19.8 - - - +
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Residues in contact with GLU 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J LEU 5.7 0.5 - - - +
279J ASN* 6.0 1.7 - - - +
147P LYS* 3.9 22.2 + - - +
148P ASN* 1.3 75.6 - - - +
150P ALA* 1.3 69.5 + - + +
152P ARG* 3.4 35.1 - - - +
153P GLU* 3.5 17.8 + - - +
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Residues in contact with ALA 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P GLY* 4.6 23.1 - - - +
129P LYS* 5.8 6.3 - - - -
147P LYS 5.1 1.3 + - - +
148P ASN 3.1 1.8 + - - -
149P GLU* 1.3 82.6 - - + +
151P LEU* 1.3 66.0 + - + +
153P GLU* 3.5 28.3 + - - +
154P LEU* 3.9 11.3 + - - +
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Residues in contact with LEU 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P TYR* 3.6 33.4 - - + -
127P GLU* 4.3 12.1 - - - +
130P LYS* 6.5 1.1 - - + -
148P ASN* 3.3 11.6 + - - +
150P ALA* 1.3 76.2 - - + +
152P ARG* 1.3 67.6 + - - +
154P LEU* 3.0 20.4 + - + +
155P ARG 3.0 9.5 + - - -
178P VAL* 3.6 29.0 - - + +
181P LYS* 3.5 22.9 - - + +
182P LEU* 3.4 31.4 - - + -
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Residues in contact with ARG 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442J ASP* 3.4 28.3 + - - -
445J GLU* 5.2 1.4 + - - -
473J VAL 5.9 0.2 - - - +
474J LEU 4.1 10.8 - - - +
475J ILE* 3.9 23.3 - - - +
476J PRO* 3.6 32.8 - - + +
477J GLN* 5.7 2.0 - - - +
148P ASN* 3.5 23.1 + - - +
149P GLU* 3.4 27.3 - - - +
151P LEU* 1.3 78.8 - - - +
153P GLU* 1.3 63.2 + - + +
155P ARG* 3.1 12.4 + - - +
156P VAL* 3.0 30.5 + - + +
182P LEU* 4.6 2.4 - - - +
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Residues in contact with GLU 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248J LYS* 3.4 39.8 + - + +
122P ARG* 4.1 23.3 + - - +
149P GLU* 3.6 16.5 - - - +
150P ALA* 3.5 17.4 + - - +
151P LEU 3.2 0.6 - - - -
152P ARG* 1.3 78.9 - - + +
154P LEU* 1.3 59.4 + - + +
156P VAL* 3.5 8.0 + - - +
157P GLU* 3.1 30.7 + - - +
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Residues in contact with LEU 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119P MET* 4.1 19.1 - - + +
122P ARG* 3.8 39.9 - - + +
123P TYR* 3.6 39.9 - - + +
150P ALA 3.9 12.3 - - - +
151P LEU* 3.0 13.6 + - + +
153P GLU* 1.3 79.2 - - + +
155P ARG* 1.3 56.7 + - - +
157P GLU* 3.2 6.1 + - - +
158P LEU* 2.8 43.3 + - + +
174P LEU* 4.6 5.4 - - + -
178P VAL* 4.1 19.5 - - + -
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Residues in contact with ARG 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439J VAL 5.6 1.0 + - - -
440J THR* 4.2 11.3 + - - +
473J VAL* 3.6 40.6 + - - +
474J LEU* 5.1 10.7 + - - +
476J PRO* 5.2 0.6 - - - +
151P LEU 3.0 11.9 + - - +
152P ARG* 3.1 9.7 + - - +
154P LEU* 1.3 76.5 - - - +
156P VAL* 1.3 80.5 + - - +
158P LEU* 4.7 0.9 - - - -
159P SER* 2.9 54.0 + - - -
175P TYR* 4.1 16.3 + - + -
178P VAL* 4.1 9.1 - - + +
179P LEU* 4.0 25.8 - - + +
182P LEU* 4.0 25.4 - - + -
184P LEU* 4.3 4.0 - - - -
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Residues in contact with VAL 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440J THR* 3.4 32.1 - - + +
442J ASP* 6.5 0.9 - - + -
474J LEU* 6.0 1.6 - - + -
152P ARG* 3.0 20.8 + - + +
153P GLU* 3.7 9.0 - - - +
155P ARG* 1.3 91.6 - - - +
157P GLU* 1.3 64.9 + - + +
159P SER* 2.7 21.4 + - - -
160P LYS* 3.3 24.3 + - - +
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Residues in contact with GLU 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252J LYS* 5.1 9.5 + - - -
115P TYR* 4.6 7.2 + - - +
118P TYR* 4.3 9.2 + - - -
119P MET* 3.5 22.0 - - + +
122P ARG* 3.3 30.3 + - - +
153P GLU 3.1 17.0 + - - +
154P LEU 3.2 2.9 + - - +
156P VAL* 1.3 76.1 - - + +
158P LEU* 1.3 63.6 + - - +
160P LYS* 3.2 17.8 + - - +
161P LEU* 3.2 28.6 + - - +
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Residues in contact with LEU 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P TYR* 4.3 12.1 - - + +
119P MET* 3.8 25.6 - - + -
154P LEU* 2.8 31.8 + - + +
157P GLU* 1.3 73.5 - - - +
159P SER* 1.3 59.2 + - - +
161P LEU* 3.2 4.4 + - + +
162P HIS* 2.9 29.8 + - - +
167P LEU* 4.1 29.5 - - + +
171P GLY* 4.8 2.7 - - - +
174P LEU* 3.3 31.4 - - + +
175P TYR* 3.6 36.1 - - + -
178P VAL* 4.6 4.0 - - + -
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Residues in contact with SER 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440J THR* 5.0 2.4 + - - -
155P ARG* 2.9 32.4 + - - -
156P VAL* 2.7 24.9 + - - +
158P LEU* 1.3 75.3 - - - +
160P LYS* 1.3 62.2 + - - +
162P HIS* 3.2 3.1 + - - +
163P GLN* 2.9 28.3 + - - +
175P TYR* 3.6 23.5 - - - -
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Residues in contact with LYS 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J MET* 6.3 0.8 - - - +
440J THR* 5.2 11.9 - - - -
156P VAL* 3.3 25.2 + - - +
157P GLU* 3.2 19.1 + - - +
159P SER* 1.3 82.4 + - - +
161P LEU* 1.3 66.4 + - + +
163P GLN* 3.6 12.3 + - - +
164P ALA* 3.1 24.0 + - - +
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Residues in contact with LEU 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P TYR* 2.7 49.4 - - + +
157P GLU* 3.2 21.0 + - + +
158P LEU* 3.2 9.7 + - + +
160P LYS* 1.3 82.9 - - + +
162P HIS* 1.3 58.2 + - - +
164P ALA* 3.3 5.7 + - - +
165P ARG 2.9 22.9 + - - -
166P GLU* 3.2 50.8 + - + +
167P LEU* 4.2 16.8 - - + +
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Residues in contact with HIS 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158P LEU 2.9 16.4 + - - +
159P SER* 3.6 4.6 + - - +
161P LEU* 1.3 77.6 - - - +
163P GLN* 1.3 63.7 + - - +
165P ARG* 3.0 19.8 + - + +
167P LEU* 4.0 14.8 - - + +
172P LEU* 4.2 29.0 - - + +
175P TYR* 3.6 29.4 + + + -
187P GLU* 6.1 0.2 - - - -
191P VAL* 4.7 12.3 - - + -
194P GLU* 5.1 7.0 - - + +
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Residues in contact with GLN 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437J ASN* 5.4 7.1 + - - +
438J GLU* 3.1 32.1 + - - +
159P SER 2.9 17.1 + - - +
160P LYS* 3.9 11.0 + - - +
162P HIS* 1.3 81.3 + - - +
164P ALA* 1.3 61.3 + - - +
165P ARG* 3.1 12.1 + - - +
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Residues in contact with ALA 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P LYS 3.1 17.3 + - - +
161P LEU 3.3 4.2 + - - +
163P GLN* 1.3 77.1 - - - +
165P ARG* 1.3 68.4 + - - +
166P GLU* 3.3 26.1 + - + +
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Residues in contact with ARG 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P LEU 2.9 4.4 + - - -
162P HIS* 3.0 15.3 + - + +
163P GLN 3.5 14.6 - - - +
164P ALA* 1.3 78.6 - - - +
166P GLU* 1.3 62.4 + - - +
167P LEU 3.5 8.6 - - - +
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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
------------------------------------------------------------
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