Contacts of the strand formed by residues 181 - 189 (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 LYS 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 5.3 10.3 + - - +
69A LYS* 5.5 3.6 - - - +
71A LYS* 5.5 1.8 - - - +
87A ILE* 4.8 2.5 - - - -
110A VAL 3.7 1.0 - - - +
111A ALA* 3.5 1.7 - - - +
112A GLU* 2.7 81.7 + - + +
173A PHE* 4.8 2.8 - - - -
179A GLY 3.9 10.3 - - - +
180A ALA* 1.3 78.3 - - - +
182A VAL* 1.3 63.6 + - - +
183A THR* 4.9 6.6 + - - +
197A GLU* 3.2 35.6 + - + +
198A LEU 3.1 15.5 - - - +
199A GLY* 4.1 3.8 - - - -
200A ALA 4.8 0.2 - - - +
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Residues in contact with VAL 182 (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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87A ILE* 4.5 3.8 - - + -
109A VAL* 4.1 15.0 - - + -
110A VAL 3.1 7.9 - - - +
111A ALA* 4.4 4.3 - - + -
128A VAL* 4.1 19.1 - - + -
169A THR* 4.5 12.3 - - + -
171A ALA* 3.1 34.5 - - + -
173A PHE* 4.3 8.7 - - + -
181A LYS* 1.3 76.7 - - - +
183A THR* 1.3 75.1 + - - +
184A VAL* 4.7 2.2 - - + -
196A GLY 4.0 0.2 - - - +
197A GLU* 3.3 4.2 - - - +
198A LEU* 2.8 43.7 + - + +
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Residues in contact with THR 183 (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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66A CYS* 5.5 1.1 - - - -
69A LYS* 6.1 1.8 - - - -
108A LEU 3.8 0.2 - - - +
109A VAL* 3.2 9.5 - - - +
110A VAL* 2.7 48.6 + - + +
112A GLU* 5.6 1.2 + - - +
181A LYS* 4.9 8.3 + - - +
182A VAL* 1.3 77.3 + - - +
184A VAL* 1.3 69.8 + - - +
185A MET* 4.0 11.2 - - + -
195A CYS* 4.0 24.2 - - + -
196A GLY 3.4 9.6 - - - +
197A GLU* 3.5 20.6 + - + +
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Residues in contact with VAL 184 (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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91A LEU* 4.0 16.6 - - + -
93A PHE* 5.4 1.1 - - + -
107A VAL* 4.7 9.6 - - + -
108A LEU 3.5 4.7 - - - +
109A VAL* 4.6 14.1 - - + -
130A LEU* 4.4 26.5 - - + -
167A MET* 6.4 1.8 - - - -
169A THR* 4.6 10.3 - - + +
182A VAL* 4.7 2.0 - - + -
183A THR* 1.3 79.2 - - - +
185A MET* 1.3 64.0 + - - +
186A ILE* 3.5 27.1 + - + +
194A TRP 3.5 1.7 - - - +
195A CYS* 3.4 1.6 - - - -
196A GLY 2.7 42.0 + - - +
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Residues in contact with MET 185 (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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37A LEU* 4.7 6.5 - - + -
62A LEU* 3.4 41.3 - - + +
65A LEU* 3.8 25.8 - - + -
66A CYS* 4.3 9.2 - - - -
107A VAL* 3.3 11.4 - - - +
108A LEU* 2.7 63.8 + - + +
110A VAL* 4.7 9.2 - - + -
183A THR* 4.3 10.3 - - + -
184A VAL* 1.3 71.5 - - - +
186A ILE* 1.3 60.6 + - - +
187A PRO* 3.7 3.0 - - - +
193A THR* 4.4 9.4 - - + -
194A TRP 3.8 3.1 - - - -
195A CYS* 3.5 16.8 - - - -
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Residues in contact with ILE 186 (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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93A PHE* 3.3 38.6 - - + -
105A VAL* 4.4 7.0 - - + -
107A VAL* 4.1 12.3 - - + -
163A VAL* 4.0 15.7 - - + -
184A VAL* 3.5 23.8 - - + +
185A MET* 1.3 79.0 - - - +
187A PRO* 1.3 64.4 - - + +
188A TYR* 3.6 30.3 + - + +
193A THR* 4.0 2.2 - - - +
194A TRP* 2.7 58.1 + - + +
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Residues in contact with PRO 187 (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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37A LEU* 3.5 39.5 - - + +
105A VAL* 3.8 28.0 - - + +
106A ARG 3.9 11.9 - - - +
160A LYS* 5.2 4.9 - - - -
185A MET 3.7 8.3 - - - +
186A ILE* 1.3 83.7 - - - +
188A TYR* 1.3 64.2 + - - +
189A SER* 3.5 6.7 - - - +
190A SER* 6.2 0.2 - - - -
192A PHE 3.4 8.5 - - - +
193A THR* 3.9 15.9 - - + +
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Residues in contact with TYR 188 (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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93A PHE* 4.1 18.0 - - - +
94A PRO* 3.6 34.5 - - + +
95A SER* 4.2 11.6 + - - -
96A VAL 4.6 2.5 - - - -
97A GLY* 5.1 6.3 - - - -
160A LYS* 3.8 19.2 + - - +
163A VAL* 4.4 7.5 + - + +
186A ILE* 3.6 33.3 - - + +
187A PRO* 1.3 74.1 - - - +
189A SER* 1.3 61.3 + - - +
192A PHE* 3.0 12.8 + + + -
194A TRP* 3.9 16.6 - + + -
297A MET* 3.5 41.1 - - + -
317A HIS* 3.8 36.7 + + + +
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Residues in contact with SER 189 (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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187A PRO* 4.5 6.6 - - - +
188A TYR* 1.3 79.3 + - - +
190A SER* 1.3 55.2 + - - +
191A THR* 2.7 32.2 + - - -
192A PHE* 2.7 33.1 + - - +
193A THR* 5.1 0.3 + - - -
297A MET* 6.3 0.4 - - - -
317A HIS* 3.7 23.1 - - - -
318A CYS* 4.9 4.3 - - - -
319A ALA* 4.9 4.5 + - - -
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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