Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 1UD8
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 GLU 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A GLN* 4.5 4.0 + - - -
133A TYR* 4.5 3.5 + - - -
165A TRP* 3.0 20.6 - - - -
166A ASP* 3.2 27.7 + - - +
169A TYR* 3.5 26.8 - - + +
170A GLN* 1.3 80.5 - - - +
172A ASN* 1.3 60.5 + - - +
173A HIS* 3.1 32.3 + - + +
175A PHE* 4.5 0.3 - - - -
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Residues in contact with ASN 172 (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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164A ASP* 3.1 27.3 + - - +
165A TRP* 3.3 30.1 - - - +
171A GLU* 1.3 72.8 - - - +
173A HIS* 1.3 77.9 + - - +
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Residues in contact with HIS 173 (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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119A GLN* 3.1 39.5 + - + +
129A ILE* 5.0 5.0 - - + +
163A VAL 3.5 0.2 - - - +
164A ASP* 2.9 30.9 + - - -
171A GLU* 3.1 38.6 + - + +
172A ASN* 1.3 90.0 + - - +
174A ILE* 1.3 64.6 + - - +
175A PHE* 3.3 38.0 + + + -
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Residues in contact with ILE 174 (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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119A GLN* 3.9 1.0 - - - -
120A VAL* 2.9 55.1 + - + +
122A PRO* 4.4 27.8 - - + +
125A ARG* 4.3 18.2 - - + +
163A VAL 4.0 1.3 - - - -
164A ASP* 4.0 11.4 - - + -
173A HIS* 1.3 73.6 - - - +
175A PHE* 1.3 57.1 + - - +
182A TRP* 4.4 5.2 - - + -
195A TYR* 3.7 48.5 - - + -
196A LEU 5.5 0.9 - - - +
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Residues in contact with PHE 175 (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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117A ALA* 4.0 15.9 - - + -
118A VAL 3.5 12.8 - - - -
119A GLN* 3.6 15.5 - - + -
133A TYR* 2.8 34.8 - + - -
135A ILE* 4.0 23.6 - - + -
162A GLY* 2.9 26.3 - - - -
163A VAL* 2.8 23.9 + - + +
165A TRP 4.3 5.6 - - - -
166A ASP* 3.5 36.1 - - + -
171A GLU 4.5 0.2 - - - -
173A HIS* 3.4 40.6 - + + -
174A ILE* 1.3 72.2 - - - +
176A ARG* 1.3 60.2 + - - +
177A PHE* 5.4 0.7 - - + -
182A TRP* 3.8 6.0 - - - -
195A TYR* 5.2 0.2 - - - -
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Residues in contact with ARG 176 (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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117A ALA* 3.4 1.7 - - - -
118A VAL* 3.1 51.2 + - + +
120A VAL* 4.0 9.1 - - + +
125A ARG 5.2 1.2 + - - -
126A TRP 5.3 1.0 + - - -
128A ASP* 3.2 34.2 + - - -
161A ASN 3.5 7.4 - - - +
174A ILE 3.9 1.4 + - - -
175A PHE* 1.3 73.0 - - - +
177A PHE* 1.3 72.2 + - - +
178A ALA* 3.2 2.1 + - - +
179A ASN* 4.4 14.1 - - - +
180A THR* 2.9 26.4 + - - +
181A ASN* 4.7 1.1 - - - +
182A TRP* 3.4 53.3 - - + +
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Residues in contact with PHE 177 (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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115A VAL* 3.8 19.5 - - + -
116A GLN 3.6 5.8 - - - +
117A ALA* 4.4 5.4 - - + +
135A ILE* 4.6 3.1 - - + -
137A ALA* 4.4 6.1 - - + -
139A THR* 3.9 22.0 - - + -
157A TRP* 3.2 46.0 - + + -
160A PHE* 3.4 27.8 - - + -
161A ASN* 2.7 14.6 + - - +
162A GLY* 3.9 16.2 - - - -
163A VAL* 4.2 23.6 - - + -
175A PHE 4.7 1.1 - - - -
176A ARG* 1.3 75.0 + - - +
178A ALA* 1.3 65.0 + - - +
179A ASN 3.5 0.2 + - - -
180A THR* 2.5 43.8 + - + +
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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