Contacts of the strand formed by residues 140 - 145 (chain L) in PDB entry 3STJ
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 PHE 140 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K PRO* 3.2 35.7 + - + -
14K SER* 3.7 18.4 - - - -
15K LEU* 3.8 25.1 - - + -
156K SER* 5.3 3.1 - - - -
138L GLY 4.4 0.2 - - - -
139L ASP* 1.3 76.9 - - - +
141L ALA* 1.3 59.7 + - - +
156L SER* 5.7 4.0 - - - +
157L GLY 3.6 8.3 - - - +
158L ILE* 3.7 23.6 - - + -
159L VAL* 5.2 0.4 - - - +
193L ASN* 3.9 19.6 - - - +
194L LEU* 3.8 33.8 + - + +
199L ILE* 4.9 2.8 - - - +
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Residues in contact with ALA 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L ASP 3.8 0.4 + - - -
140L PHE* 1.3 75.8 - - - +
142L VAL* 1.3 64.3 + - - +
143L ALA 4.2 0.4 + - - -
156L SER* 3.6 3.5 + - - -
157L GLY 2.9 34.9 + - - +
158L ILE 4.5 7.0 - - - -
159L VAL* 4.5 4.0 - - + -
178L THR* 4.1 13.2 - - - +
180L ALA* 4.5 1.0 - - - +
191L LEU* 3.8 25.1 - - + -
192L LEU 3.3 10.3 - - - +
199L ILE* 4.2 9.2 - - + -
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Residues in contact with VAL 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J ILE* 4.9 2.5 - - + -
15L LEU* 3.8 27.8 - - + -
18L MET* 3.8 23.1 - - + -
19L LEU* 4.1 24.9 - - + -
141L ALA* 1.3 77.2 - - - +
143L ALA* 1.3 64.9 + - - +
144L VAL* 4.1 6.1 - - + -
154L ALA* 4.2 9.6 - - + -
155L THR 3.3 13.2 - - - +
156L SER* 4.6 2.9 - - - +
190L ALA 3.5 2.8 - - - +
191L LEU* 3.5 2.9 - - - -
192L LEU* 2.7 44.5 + - + +
193L ASN 5.0 0.2 - - - +
194L LEU* 4.9 6.5 - - + -
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Residues in contact with ALA 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L ALA 4.2 0.4 - - - -
142L VAL* 1.3 71.4 - - - +
144L VAL* 1.3 59.6 + - - +
145L GLY 4.2 0.4 - - - -
153L THR 3.7 1.4 - - - +
154L ALA* 3.4 4.7 - - - -
155L THR* 2.8 49.9 + - - +
180L ALA* 3.9 11.1 - - + +
181L SER 4.4 0.4 - - - +
182L ILE* 3.9 19.3 - - + -
186L ASN* 4.7 4.0 - - - +
190L ALA 3.4 5.6 - - - -
191L LEU* 4.1 8.9 - - + +
202L ASN* 3.9 13.7 - - - +
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Residues in contact with VAL 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L LEU* 4.5 0.7 - - + -
23L LEU* 3.7 31.2 - - + -
26L VAL* 3.5 25.8 - - + +
142L VAL* 4.1 11.7 - - + -
143L ALA* 1.3 79.1 - - - +
145L GLY* 1.3 60.8 + - - +
152L GLN* 3.7 18.8 - - + -
153L THR 3.5 6.1 - - - +
154L ALA* 4.5 2.0 - - + -
186L ASN* 4.1 2.7 - - - -
189L GLY* 3.4 4.9 - - - -
190L ALA* 2.7 37.3 + - + +
192L LEU* 3.6 30.5 - - + -
202L ASN* 4.0 1.5 + - - +
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Residues in contact with GLY 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L VAL* 4.8 2.7 - - - -
66L SER* 3.3 15.7 - - - -
144L VAL* 1.3 77.9 - - - +
146L ASN* 1.3 56.9 + - - -
147L PRO* 3.4 8.1 - - - +
152L GLN* 3.4 6.3 - - - -
153L THR 2.8 36.0 + - - +
186L ASN* 3.6 13.6 + - - -
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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
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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