Contacts of the strand formed by residues 149 - 154 (chain B) in PDB entry 5JLH
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 GLY 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 4.4 6.1 - - - -
148B THR* 1.3 81.5 - - - +
150B ILE* 1.3 60.4 + - - -
151B VAL* 3.9 4.0 - - - +
162B VAL 4.0 1.0 - - - +
163B PRO 3.7 0.2 - - - -
164B ILE* 2.8 32.8 + - - +
292B LEU* 3.4 10.1 - - - -
295B ASN* 3.3 20.6 - - - -
297B VAL* 5.1 0.7 - - - -
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY* 1.3 74.8 - - - -
151B VAL* 1.3 63.6 + - - +
152B MET 3.5 2.1 + - - +
161B THR* 3.7 19.7 - - + -
162B VAL 3.7 2.0 - - - -
163B PRO* 3.9 19.3 - - + -
277B THR* 4.0 11.2 - - + -
280B SER* 3.6 31.6 - - - -
281B ILE* 3.7 25.8 - - + -
292B LEU* 3.6 19.0 - - + +
295B ASN 3.6 3.6 + - - -
296B THR* 3.3 31.2 - - + +
297B VAL 3.0 17.4 + - - -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 3.7 27.9 - - + +
140B SER* 3.2 22.2 - - - +
141B LEU* 3.9 34.8 - - + -
149B GLY 4.8 1.1 - - - +
150B ILE* 1.3 75.4 - - - +
152B MET* 1.3 61.6 + - - +
153B ASP 3.7 1.3 + - - +
160B HIS 3.8 0.5 - - - +
161B THR* 3.4 5.5 - - - -
162B VAL 3.0 33.6 + - - +
164B ILE* 5.7 1.1 - - + -
297B VAL* 3.3 23.1 - - + +
299B SER* 4.2 13.0 - - - +
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Residues in contact with MET 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ILE* 3.5 3.6 + - + +
151B VAL* 1.3 70.0 - - - +
153B ASP* 1.3 58.6 + - - +
154B SER* 4.7 8.5 - - - +
159B THR* 3.3 27.8 - - + -
160B HIS 3.7 2.5 - - - +
161B THR* 3.6 22.9 - - + +
273B ILE* 3.6 39.3 - - + +
276B THR* 4.9 0.9 - - - +
277B THR* 4.3 16.6 - - + +
296B THR* 4.9 5.6 - - + -
297B VAL 2.8 7.9 + - - +
298B LEU* 3.5 29.7 - - + +
299B SER* 2.8 29.8 + - - +
303B THR* 4.7 6.7 - - + +
312B MET* 5.1 5.2 - - + -
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Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PRO* 4.4 2.1 - - - +
136B GLN* 2.9 38.1 - - - +
137B ALA* 4.5 9.2 + - + +
151B VAL* 3.7 10.0 + - + -
152B MET* 1.3 72.4 - - - +
154B SER* 1.3 62.6 + - - +
155B GLY 3.8 9.4 + - - -
158B VAL 4.5 0.3 - - - +
159B THR* 3.2 1.7 - - - +
160B HIS* 2.5 68.0 + - + +
299B SER* 3.4 18.1 + - - +
300B GLY* 4.8 0.9 - - - -
338B VAL* 5.3 1.2 - - - +
402B MG 4.0 7.4 - - - -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B MET* 3.9 8.2 + - - +
153B ASP* 1.3 76.0 + - - +
155B GLY* 1.3 59.7 + - - +
159B THR* 3.1 31.2 - - - +
260B LEU* 5.7 2.9 - - - +
299B SER 3.4 4.8 + - - -
300B GLY* 3.2 22.7 - - - -
302B THR* 3.0 25.6 + - - +
303B THR* 3.4 20.6 - - - +
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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