Contacts of the strand formed by residues 168 - 173 (chain A) in PDB entry 1ML0
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A THR* 3.5 23.1 - - - +
89A GLY* 3.9 5.6 - - - +
90A ARG* 3.8 34.8 - - + +
129A GLU 3.6 1.2 - - - +
130A LEU* 3.2 6.8 - - - +
131A GLN* 2.8 55.3 + - + +
166A GLY 3.4 4.0 + - - +
167A MET* 1.3 75.0 - - - +
169A THR* 1.3 65.8 + - - +
170A ARG* 3.1 36.1 - - - +
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Residues in contact with THR 169 (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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88A THR* 3.2 6.3 + - - -
89A GLY 2.8 45.8 + - - -
91A LEU* 4.2 20.0 + - + +
93A PHE* 5.5 2.1 - - - -
128A VAL* 4.5 12.8 - - + -
129A GLU 3.9 2.2 - - - -
130A LEU* 3.6 23.0 - - + +
167A MET* 4.3 4.0 + - - +
168A LEU* 1.3 73.7 - - - +
170A ARG* 1.3 64.3 + - - +
171A ALA 5.2 0.2 - - - +
182A VAL* 4.5 11.2 - - + -
184A VAL* 4.6 5.9 - - + +
198A LEU* 3.6 23.6 - - + +
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Residues in contact with ARG 170 (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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86A ILE* 3.8 26.9 - - + -
87A ILE 3.6 3.4 - - - +
88A THR* 4.2 9.5 + - - +
127A TYR 3.4 2.6 - - - +
128A VAL* 3.3 6.0 - - - -
129A GLU* 3.0 67.8 + - + +
131A GLN* 2.9 39.9 + - - +
136A THR* 5.3 0.2 - - - +
168A LEU* 3.1 21.1 - - - +
169A THR* 1.3 76.6 - - - +
171A ALA* 1.3 62.2 + - - +
172A THR* 4.3 6.7 - - - +
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Residues in contact with ALA 171 (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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86A ILE* 3.3 2.9 - - - +
87A ILE* 2.8 45.9 + - + +
126A ALA* 5.7 0.4 - - + -
127A TYR 3.5 4.5 - - - -
128A VAL* 4.4 7.4 - - + +
169A THR* 4.4 1.5 - - + +
170A ARG* 1.3 74.7 - - - +
172A THR* 1.3 60.7 + - - +
173A PHE* 3.6 16.5 - - + -
182A VAL* 3.1 36.3 - - + -
198A LEU* 6.0 0.7 - - + -
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Residues in contact with THR 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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84A GLN* 3.8 22.7 - - + +
85A GLU 3.9 2.5 - - - -
86A ILE* 3.3 36.4 - - + +
125A TYR* 3.9 10.2 - - + -
126A ALA* 3.3 5.2 - - - -
127A TYR* 3.0 42.4 + - + +
129A GLU* 4.4 4.8 + - - -
170A ARG* 4.3 7.3 - - - +
171A ALA* 1.3 73.3 - - - +
173A PHE* 1.3 73.0 + - - +
174A LEU* 5.8 0.7 - - + -
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Residues in contact with PHE 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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76A TRP* 3.4 20.6 - + - -
84A GLN* 3.3 8.3 - - - +
85A GLU 2.8 26.5 + - - +
87A ILE* 3.7 18.4 - - + -
111A ALA* 4.8 2.5 - - + -
112A GLU 4.6 5.2 - - - -
124A PHE* 3.8 17.7 - + - -
125A TYR* 3.2 21.5 - - - -
126A ALA* 3.6 19.5 - - + -
171A ALA* 3.6 29.4 - - + -
172A THR* 1.3 80.0 - - - +
174A LEU* 1.3 68.1 + - - +
175A GLU 3.3 18.2 - - - +
177A TRP* 3.5 19.1 - + + +
180A ALA* 4.5 14.1 - - + -
181A LYS 4.8 1.6 - - - -
182A VAL* 4.3 10.8 - - + -
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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