Contacts of the strand formed by residues 140 - 145 (chain B) in PDB entry 1UU1
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 ASP 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE* 4.0 2.6 - - - -
97B ASP* 5.6 0.2 - - - +
98B ARG* 2.6 58.9 + - - +
100B VAL* 4.2 10.3 - - + -
136B VAL* 3.4 9.9 - - + -
137B GLY 2.9 31.0 + - - +
139B GLY* 1.3 84.3 + - - +
141B VAL* 1.3 62.8 + - - +
142B VAL* 4.1 0.9 - - + -
168B ALA* 4.1 2.2 - - + -
169B PHE* 3.1 28.0 + - - +
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Residues in contact with VAL 141 (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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92B MET* 3.9 18.4 - - + +
93B MET* 5.2 0.2 - - - -
96B PHE* 3.0 55.2 - - + -
98B ARG 2.9 8.5 + - - +
99B SER* 3.6 14.0 - - - +
100B VAL* 2.8 27.4 + - - +
140B ASP* 1.3 74.1 - - - +
142B VAL* 1.3 61.9 + - - +
143B PHE* 3.9 14.5 + - + -
169B PHE* 3.2 20.0 - - + +
171B ALA* 4.4 7.2 - - + -
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Residues in contact with VAL 142 (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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100B VAL* 3.4 19.7 - - + +
102B PHE* 3.7 24.0 - - + -
134B VAL* 6.2 0.2 - - + -
136B VAL* 4.2 17.0 - - + -
140B ASP* 4.9 0.7 - - + -
141B VAL* 1.3 77.0 - - - +
143B PHE* 1.3 61.2 + - - +
144B ILE* 3.5 30.1 + - + +
163B ILE* 3.7 24.9 - - + -
168B ALA* 4.3 11.2 - - + -
169B PHE 2.7 12.7 + - - +
170B VAL* 3.6 2.7 - - + -
171B ALA* 2.9 24.2 + - - -
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Residues in contact with PHE 143 (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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89B ILE* 3.9 32.3 - - + -
92B MET* 4.0 14.4 - - + -
93B MET* 3.9 25.4 - - + -
99B SER* 3.6 34.1 - - - -
100B VAL 2.8 13.4 + - - +
101B PHE* 3.9 26.9 - + + +
102B PHE* 4.4 4.9 + - - -
105B THR* 4.8 0.3 + - - -
109B TYR* 3.6 35.0 - + + -
141B VAL* 4.2 15.7 - - + -
142B VAL* 1.3 69.9 - - - +
144B ILE* 1.3 63.9 + - - +
145B PRO* 3.7 7.2 - - - +
171B ALA* 3.7 24.7 - - + -
173B ASP* 5.8 0.4 - - + -
197B ILE* 4.8 1.8 - - + -
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Residues in contact with ILE 144 (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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102B PHE* 4.0 8.1 - - + -
109B TYR* 4.4 0.6 + - - -
131B ILE* 4.1 8.5 - - + -
142B VAL* 3.6 18.6 - - + +
143B PHE* 1.3 79.0 - - - +
145B PRO* 1.3 68.2 - - + +
146B ASN* 3.3 2.1 + - + -
155B PHE* 3.7 37.9 - - + -
160B ILE* 4.6 13.2 - - + -
163B ILE* 3.4 31.2 - - + -
170B VAL* 4.0 18.6 - - + -
171B ALA 3.0 11.1 + - - +
172B LEU* 3.6 17.2 - - + +
173B ASP* 3.0 19.4 + - - -
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Residues in contact with PRO 145 (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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102B PHE* 6.5 0.4 - - + -
105B THR* 3.7 20.2 - - - +
106B TYR 4.6 2.5 - - - +
109B TYR* 3.5 15.7 - - + +
143B PHE 3.7 3.6 - - - +
144B ILE* 1.3 85.1 - - + +
146B ASN* 1.3 61.6 + - - +
147B PRO 3.3 10.1 - - - +
148B ASN* 3.0 30.3 - - - +
149B ASN 3.9 9.2 - - - +
155B PHE* 3.3 17.1 - - + -
173B ASP* 3.2 12.1 - - + +
1335B PMP 3.9 26.9 - - + -
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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