Contacts of the strand formed by residues 88 - 97 (chain F) in PDB entry 1U1C
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 THR 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F THR* 2.9 9.9 + - - -
21F LEU* 3.9 28.1 - - + +
22F ALA 2.9 27.7 + - - +
86F ILE* 3.3 5.0 - - - +
87F ARG* 1.3 81.9 - - - +
89F PHE* 1.3 66.2 + - - +
90F LEU* 4.2 1.8 - - + -
136F CYS* 3.7 28.0 - - - -
212F ARG* 3.0 36.8 + - + +
252F LEU* 4.5 4.5 - - + -
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Residues in contact with PHE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ALA* 3.5 3.6 - - + +
24F VAL* 4.2 20.2 - - + -
78F VAL* 3.4 42.8 - - + -
81F LEU* 3.7 26.7 - - + -
82F ALA 4.1 3.4 - - - -
86F ILE* 3.5 40.4 - - + -
87F ARG 4.4 1.6 - - - -
88F THR* 1.3 76.7 - - - +
90F LEU* 1.3 63.5 + - - +
91F ARG 4.0 0.4 - - - -
202F LEU* 3.9 18.1 - - + +
206F CYS* 3.8 17.5 - - - -
211F LEU* 4.2 15.3 - - + -
212F ARG 2.8 13.4 + - - +
213F ALA* 3.1 5.1 - - + +
214F GLY 2.9 25.3 + - - +
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU* 4.3 9.6 - - + -
22F ALA 2.9 12.9 + - - +
23F ILE* 3.3 9.4 - - + +
24F VAL* 2.8 25.6 + - - +
88F THR* 4.8 2.2 - - + -
89F PHE* 1.3 78.2 - - - +
91F ARG* 1.3 63.5 + - - +
92F ILE 3.6 0.9 + - - -
136F CYS* 4.0 9.4 - - + -
140F LEU* 4.3 12.3 - - + -
214F GLY* 3.8 19.7 - - - +
245F VAL* 3.8 23.8 - - + +
248F ALA* 4.2 4.0 - - + -
249F ALA* 3.8 37.9 - - + +
252F LEU* 3.9 24.5 - - + -
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F VAL* 3.4 17.9 + - + +
25F PRO 4.5 0.2 - - - -
26F GLY* 3.9 5.7 - - - +
67F THR* 4.9 3.3 + - - -
74F THR* 5.9 1.3 - - - -
89F PHE 4.0 0.4 - - - -
90F LEU* 1.3 72.6 - - - +
92F ILE* 1.3 65.0 + - - +
93F GLY* 3.7 10.6 - - - -
140F LEU* 5.6 0.2 - - - +
196F GLU* 2.8 36.9 + - - +
198F GLU* 2.9 35.3 + - - +
199F SER 4.4 4.3 - - - +
202F LEU* 3.7 26.2 - - + +
214F GLY 3.0 9.0 + - - +
215F MET* 3.3 23.8 - - - +
216F VAL* 3.0 33.4 + - - +
245F VAL* 4.4 0.8 - - - +
3052F PO4 2.8 43.8 + - - -
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Residues in contact with ILE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ILE* 3.7 26.9 - - + -
24F VAL 3.5 1.2 + - - -
25F PRO* 3.3 19.8 - - + +
30F ARG* 2.8 27.5 + - - +
34F ILE* 3.8 17.7 - - + -
91F ARG* 1.3 76.6 + - - +
93F GLY* 1.3 62.7 + - - +
216F VAL* 3.4 11.7 - - + +
241F ALA* 3.4 50.0 - - + +
242F VAL* 3.7 15.0 - - + +
245F VAL* 4.0 11.9 - - + -
3052F PO4 3.5 1.9 + - - -
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Residues in contact with GLY 93 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F ARG* 3.9 2.5 - - - -
91F ARG* 3.7 12.6 - - - +
92F ILE* 1.3 80.2 - - - +
94F THR* 1.3 66.4 + - - +
216F VAL 3.0 11.6 + - - -
217F ALA* 3.3 5.9 - - - -
218F GLY* 3.2 21.3 + - - -
241F ALA* 5.3 0.5 - - - +
3052F PO4 3.2 15.7 - - - -
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Residues in contact with THR 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ARG* 4.1 5.3 + - - +
30F ARG* 3.5 14.8 - - - +
93F GLY* 1.3 78.1 - - - +
95F THR* 1.3 65.4 + - - +
196F GLU* 3.6 7.6 - - - +
217F ALA* 4.5 0.5 - - - +
218F GLY 3.8 7.2 - - - -
220F ILE* 4.3 19.5 - - + +
238F GLU* 3.7 28.0 - - - +
3052F PO4 2.7 35.7 + - - +
5051F BAU 3.0 24.7 + - - -
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F THR* 1.3 79.5 - - - +
96F GLY* 1.3 59.9 + - - +
108F LEU* 3.8 19.7 - - + -
194F ASN* 2.6 34.7 + - + +
195F TYR 2.7 19.7 + - - -
196F GLU* 4.5 1.6 - - - -
217F ALA* 4.0 12.3 - - + -
218F GLY 3.2 17.1 + - - +
219F VAL* 3.8 10.3 - - + -
220F ILE* 3.3 27.8 + - - +
221F VAL 3.8 0.7 + - - -
5051F BAU 3.7 9.8 - - - -
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Residues in contact with GLY 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F THR* 1.3 75.3 + - - +
97F ALA* 1.3 65.3 + - - -
98F ILE* 4.4 1.7 - - - +
194F ASN* 3.3 1.1 - - - -
195F TYR* 2.9 34.6 + - - +
221F VAL* 3.2 12.3 - - - -
223F ARG* 4.8 5.2 - - - -
5051F BAU 3.5 26.0 - - - -
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F THR* 4.1 1.8 + - - +
96F GLY* 1.3 72.5 - - - -
98F ILE* 1.3 58.6 + - - +
99F GLN 3.7 0.2 - - - -
102F ILE* 3.8 30.7 - - + -
108F LEU* 5.0 0.2 - - + -
193F MET 3.5 9.9 - - - +
194F ASN* 4.1 3.8 - - + -
219F VAL* 3.8 17.6 - - + +
221F VAL 2.7 11.6 + - - +
222F ASN* 3.5 15.2 - - - +
223F ARG* 2.7 34.5 + - - +
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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