Contacts of the strand formed by residues 149 - 156 (chain P) in PDB entry 1IJS
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 VAL 149 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147P ASN* 4.0 10.3 - - + +
148P VAL* 1.3 81.2 - - - +
150P LEU* 1.3 65.7 + - - +
151P LYS* 3.9 33.9 - - + -
167P ASN* 4.3 4.0 - - - +
257P THR* 4.8 7.9 - - + -
525P SER* 2.9 7.6 - - - -
526P ASP* 2.9 47.3 + - + +
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Residues in contact with LEU 150 (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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148P VAL* 4.5 11.7 - - + -
149P VAL* 1.3 75.3 - - - +
151P LYS* 1.3 61.6 + - - +
167P ASN* 3.6 6.8 - - - +
168P ASP* 3.1 24.9 + - - +
169P LEU* 5.7 0.3 - - - +
171P ALA* 3.2 23.8 - - + +
172P SER* 3.1 51.6 - - - +
173P LEU* 4.0 5.4 - - + +
255P LEU 4.9 0.4 - - - +
256P ARG* 5.3 2.7 - - - -
257P THR* 5.0 6.7 + - - +
502P VAL* 4.9 2.9 - - + -
523P THR* 4.5 9.9 - - + -
524P TYR 3.5 6.5 - - - +
525P SER* 2.4 42.2 - - - +
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Residues in contact with LYS 151 (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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149P VAL* 3.9 19.7 - - + -
150P LEU* 1.3 76.2 - - - +
152P THR* 1.4 60.1 + - - +
165P TYR* 5.0 10.2 - - + +
166P ASN* 2.8 16.8 - - - +
167P ASN* 2.9 36.3 - - - +
168P ASP* 5.4 0.2 - - - -
523P THR* 3.8 4.4 - - - -
524P TYR* 3.0 67.2 + - + +
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Residues in contact with THR 152 (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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151P LYS* 1.4 72.9 - - - +
153P VAL* 1.3 71.9 - - - +
154P SER* 4.0 5.1 + - - +
164P VAL 3.9 0.9 - - - +
165P TYR* 3.6 2.8 - - - +
166P ASN* 2.8 40.5 + - - +
167P ASN 4.9 0.4 - - - -
168P ASP* 3.5 27.0 + - - +
521P ILE* 2.8 39.3 - - + +
522P VAL 3.6 6.5 - - - +
523P THR* 4.4 5.3 + - - +
524P TYR* 5.4 0.2 - - - -
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Residues in contact with VAL 153 (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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152P THR* 1.3 79.8 - - - +
154P SER* 1.3 70.8 + - - +
155P GLU* 4.0 6.6 + - + +
163P LYS* 4.5 25.4 - - + -
164P VAL 3.8 4.3 - - - +
165P TYR* 4.0 17.5 - - + -
522P VAL* 3.2 36.7 + - + +
524P TYR* 3.7 32.5 - - + -
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Residues in contact with SER 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152P THR* 4.0 6.4 + - - +
153P VAL* 1.3 75.5 - - - +
155P GLU* 1.3 60.5 + - - +
156P SER* 3.5 3.6 + - - -
163P LYS* 3.6 1.4 - - - +
164P VAL* 2.7 58.7 + - - +
166P ASN* 4.2 10.0 + - - +
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Residues in contact with GLU 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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153P VAL* 4.0 9.0 + - + +
154P SER* 1.3 70.1 - - - +
156P SER* 1.3 59.0 + - - +
157P ALA* 3.1 13.4 + - + +
161P PRO* 5.4 10.3 - - + -
162P THR 3.8 7.9 - - - +
163P LYS* 2.8 37.9 + - + +
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Residues in contact with SER 156 (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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154P SER* 3.5 3.1 + - - -
155P GLU* 1.3 68.5 - - - +
157P ALA* 1.3 53.6 + - - +
158P THR* 2.6 31.8 + - - +
161P PRO* 3.8 0.4 - - - -
162P THR* 2.8 36.0 + - - -
164P VAL* 4.4 17.5 - - - -
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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