Contacts of the strand formed by residues 139 - 144 (chain A) in PDB entry 4UAL
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 LEU 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ARG* 4.6 0.9 - - + +
128A LEU* 3.7 35.4 + - + +
129A VAL* 3.6 32.3 - - + -
137A THR 3.4 3.0 + - - -
138A ALA* 1.3 72.4 - - - +
140A HIS* 1.3 62.4 + - - +
141A TYR 3.4 22.9 - - - +
142A ALA* 4.6 1.6 - - + -
151A LEU* 4.0 23.3 - - + -
152A VAL 3.7 9.6 - - - +
153A MET* 3.9 14.6 - - + -
403A PHE* 3.6 23.2 - - + -
405A THR* 4.0 13.2 + - - +
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Residues in contact with HIS 140 (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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100A ARG* 3.4 19.7 + - - -
102A TYR* 4.0 15.4 + + + -
138A ALA* 3.9 6.5 - - + +
139A LEU* 1.3 75.8 - - - +
141A TYR* 1.3 85.6 + - + +
152A VAL 2.8 13.7 + - - +
153A MET 4.2 0.9 - - - -
154A ASP* 2.8 45.5 + - - -
403A PHE* 3.8 3.5 - - - -
404A THR* 3.7 0.5 - - - -
405A THR* 2.9 47.6 + - + +
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Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.4 36.6 - - + -
76A PHE* 4.5 1.6 - + - -
95A MET* 4.0 18.5 - - + +
102A TYR* 4.0 22.8 + + - -
139A LEU* 3.4 9.9 - - - +
140A HIS* 1.3 104.1 + + + +
142A ALA* 1.3 59.9 + - - +
143A PHE* 4.6 1.6 - - + -
150A TYR 3.9 0.3 - - - +
151A LEU* 3.6 0.2 - - - -
152A VAL* 2.9 50.7 + - + +
403A PHE 3.2 5.2 - - - +
404A THR* 4.0 20.0 - - + -
406A GLU* 2.9 38.0 + - - -
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Residues in contact with ALA 142 (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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71A LEU* 5.8 0.2 - - - +
125A ARG* 4.4 4.5 - - + -
139A LEU* 4.6 2.7 - - + -
141A TYR* 1.3 73.9 - - - +
143A PHE* 1.3 65.4 + - - +
150A TYR 3.2 6.3 - - - -
151A LEU* 3.8 14.1 - - + -
401A PHE* 3.3 35.0 - - + +
402A THR* 3.3 6.1 - - - +
403A PHE* 2.8 39.7 + - + +
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Residues in contact with PHE 143 (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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70A GLN* 6.5 0.4 - - + -
71A LEU* 3.4 42.6 - - + +
72A HIS* 3.5 33.9 - - - -
73A ARG 3.5 5.2 - - - -
76A PHE* 4.0 14.1 - + - -
104A MET* 4.1 4.9 - - + -
141A TYR* 4.6 0.7 - - + -
142A ALA* 1.3 78.5 - - - +
144A GLN* 1.3 70.7 + - - +
145A ASP* 5.6 1.3 - - + -
149A LEU* 3.6 1.6 - - - -
150A TYR* 2.8 76.4 + + + +
152A VAL* 3.9 21.3 - - + -
401A PHE* 3.7 6.0 - - - -
402A THR* 4.3 15.0 - - + +
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Residues in contact with GLN 144 (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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32A ASP* 3.5 22.3 + - - +
71A LEU 4.8 3.6 - - - +
72A HIS* 6.1 0.2 - - - -
109A LYS* 2.9 26.7 + - - +
143A PHE* 1.3 85.6 - - - +
145A ASP* 1.3 64.6 + - - +
148A HIS 3.2 13.2 - - - +
149A LEU* 3.8 8.1 - - + -
150A TYR* 4.2 3.8 - - - -
395A HIS* 4.8 4.2 + - - +
398A PHE* 3.0 39.0 + - - +
401A PHE* 3.9 5.8 - - + +
402A THR* 3.6 12.3 + - - +
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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