Contacts of the strand formed by residues 135 - 142 (chain G) in PDB entry 5UWC
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 GLN 135 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133G ASP 3.4 3.3 + - - +
134G VAL* 1.3 85.7 + - - +
136G TYR* 1.3 64.0 + - - +
137G ASP 4.5 0.2 + - - -
156G THR* 5.2 0.6 - - - +
160G GLY 3.1 24.2 + - - -
161G THR* 3.9 0.9 - - - +
162G ARG* 2.9 51.9 + - - +
186G GLY* 3.4 2.6 - - - -
187G ARG* 2.9 72.4 + - + +
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Residues in contact with TYR 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ALA 2.6 25.6 + - - -
106G GLY 3.7 0.7 - - - -
107G ALA* 3.4 23.6 - - + -
124G TRP* 3.7 18.8 - + + +
126G VAL* 4.1 14.8 - - + +
127G GLY* 3.2 15.5 + - - -
130G ALA* 4.0 4.3 - - - +
134G VAL* 3.4 24.8 - - + +
135G GLN* 1.3 78.1 + - - +
137G ASP* 1.3 62.0 + - - +
154G TYR* 4.1 3.3 - - - -
161G THR* 3.9 16.2 - - + -
162G ARG* 3.0 48.9 + - + +
184G VAL* 3.8 20.0 - - + -
185G ARG 3.2 16.2 - - - +
186G GLY* 3.8 6.3 - - - -
193G ILE* 4.1 8.1 - - + -
194G PRO 5.3 0.4 - - - -
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Residues in contact with ASP 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G TRP* 5.4 0.2 - - - -
136G TYR* 1.3 72.8 - - - +
138G LEU* 1.3 58.9 + - - +
139G TYR* 3.7 19.1 + - + -
150G GLU* 3.7 23.9 - - - +
154G TYR* 3.5 5.5 + - - +
162G ARG* 3.0 13.5 + - - -
183G LEU 3.5 1.0 - - - +
184G VAL* 3.2 6.7 - - - -
185G ARG* 2.9 40.2 + - + +
186G GLY 5.3 0.3 - - - -
187G ARG* 2.7 44.9 + - - +
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G LEU* 4.4 0.4 - - + -
122G CYS* 3.5 33.9 - - + -
124G TRP* 3.6 25.1 - - + -
137G ASP* 1.3 73.7 - - - +
139G TYR* 1.3 67.7 + - - +
140G LEU* 5.1 0.7 - - + -
150G GLU* 3.6 6.6 - - - +
151G CYS* 2.9 38.4 + - + -
154G TYR* 2.9 9.2 + - - +
165G CYS* 4.6 2.7 - - + -
167G PHE* 3.6 32.8 - - + -
182G ILE* 3.6 28.5 - - + -
183G LEU 3.3 4.7 - - - +
184G VAL* 4.0 9.0 - - + +
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Residues in contact with TYR 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G ASP* 3.7 25.3 + - + +
138G LEU* 1.3 77.7 - - - +
140G LEU* 1.3 59.5 + - - +
141G ASN* 5.3 1.1 - - - +
148G GLN* 3.3 42.6 - - + +
149G TYR 3.4 5.2 - - - -
150G GLU* 3.5 42.1 + - + -
181G HIS 3.9 0.5 - - - +
182G ILE* 3.4 7.3 - - - +
183G LEU* 2.9 47.9 + - + +
185G ARG* 3.3 45.4 + - + -
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G LEU* 3.7 22.2 - - + -
139G TYR* 1.3 74.0 - - - +
141G ASN* 1.3 60.3 + - - +
142G VAL* 4.9 8.1 - - + -
147G GLN 4.0 1.7 - - - +
148G GLN* 3.5 4.0 - - - -
149G TYR* 2.8 53.9 + - + +
167G PHE* 3.8 13.7 - - + -
170G ILE* 4.1 13.2 - - + -
173G LEU* 4.0 31.2 - - + -
174G SER 5.7 0.2 - - - +
180G SER* 3.1 27.6 - - - +
181G HIS 3.5 2.2 - - - -
182G ILE* 3.7 18.8 - - + +
202G PHE* 4.8 3.6 - - + -
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Residues in contact with ASN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G LEU* 5.5 3.8 - - - +
139G TYR* 4.2 1.1 - - - -
140G LEU* 1.3 69.6 - - - +
142G VAL* 1.3 62.2 + - - +
143G ALA 4.0 0.2 + - - -
146G ARG* 3.8 34.9 - - - +
147G GLN 4.4 4.4 - - - -
148G GLN* 3.1 41.5 + - - +
180G SER* 3.0 2.7 + - - -
181G HIS* 2.7 69.0 + - + +
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Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G LEU* 4.0 7.5 - - + -
141G ASN* 1.3 74.0 - - - +
143G ALA* 1.3 69.5 + - - +
144G ASN 3.3 2.1 + - - -
145G ARG* 3.2 33.3 + - + +
146G ARG* 3.1 17.9 - - - -
147G GLN 4.3 2.9 + - - +
149G TYR* 3.7 20.6 - - + -
173G LEU 3.6 14.8 - - - +
174G SER* 3.7 19.3 - - - +
177G SER* 3.2 31.4 - - - +
179G SER 3.9 5.6 - - - +
180G SER* 4.0 8.7 - - - +
202G PHE* 4.8 2.0 - - + -
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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