Contacts of the strand formed by residues 192 - 201 (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 PHE 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASN* 3.3 23.8 - - + -
68A VAL* 3.9 21.5 - - + -
94A PRO* 5.5 0.2 - - + -
187A PRO* 3.4 2.8 - - - +
188A TYR* 3.0 26.3 + + + -
189A SER* 2.7 31.6 + - - +
190A SER 3.6 0.2 - - - -
191A THR* 1.3 81.2 - - - +
193A THR* 1.3 66.5 + - - +
194A TRP* 4.0 19.5 - - + -
295A TYR* 3.6 31.6 - + + -
297A MET* 3.9 29.2 - - + -
319A ALA* 3.7 24.2 - - + -
368A MET* 3.9 18.2 - - + -
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Residues in contact with THR 193 (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* 4.5 13.3 - - + +
65A LEU* 3.4 22.9 + - - +
66A CYS* 3.7 1.6 - - - -
67A ASN* 2.7 36.3 + - - +
68A VAL 3.5 4.5 + - - -
185A MET* 4.4 13.2 - - + -
186A ILE 3.4 19.1 - - - +
187A PRO* 3.9 12.5 - - + +
189A SER 5.1 0.3 + - - -
191A THR 5.5 0.3 - - - -
192A PHE* 1.3 80.1 + - - +
194A TRP* 1.3 61.3 + - - +
195A CYS* 4.1 19.1 - - - -
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Residues in contact with TRP 194 (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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68A VAL* 3.4 31.2 - - + +
70A ASN* 3.2 27.3 - - + +
91A LEU* 4.1 9.6 - - + -
92A PRO* 3.5 31.9 - - + -
93A PHE* 3.8 21.1 - + - -
94A PRO* 3.5 22.8 - - + +
184A VAL 3.5 0.2 - - - +
186A ILE* 2.7 56.3 + - + +
188A TYR* 3.9 15.9 - + + -
192A PHE* 4.0 7.3 - - + -
193A THR* 1.3 73.2 - - - +
195A CYS* 1.3 63.0 + - - +
196A GLY* 3.6 25.8 - - - -
368A MET* 4.1 8.3 - - - -
373A GLN* 3.2 16.8 + - - -
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Residues in contact with CYS 195 (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* 2.0 50.9 - - - -
68A VAL 2.9 14.4 + - - +
69A LYS* 3.4 10.0 - - + +
70A ASN* 2.8 30.8 + - - +
183A THR* 4.0 14.6 - - + -
184A VAL 3.4 2.5 - - - -
185A MET* 3.5 24.5 - - - -
193A THR* 4.1 4.5 - - - -
194A TRP* 1.3 80.2 - - - +
196A GLY* 1.3 61.6 + - - +
197A GLU 3.6 0.5 + - - -
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Residues in contact with GLY 196 (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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70A ASN 3.6 2.5 - - - -
91A LEU* 3.5 29.9 - - - +
182A VAL 4.0 0.3 - - - +
183A THR* 3.4 1.4 - - - -
184A VAL* 2.7 42.3 + - - +
194A TRP* 3.6 19.2 - - - -
195A CYS* 1.3 72.7 - - - +
197A GLU* 1.3 57.7 + - - -
198A LEU* 5.7 0.3 - - - +
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Residues in contact with GLU 197 (chain A).
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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69A LYS* 2.7 40.6 + - + -
70A ASN 2.9 11.6 + - - +
71A LYS* 3.3 38.3 + - + -
72A MET* 3.1 31.9 + - - +
91A LEU* 4.1 1.4 - - - +
181A LYS* 3.2 34.4 + - + +
182A VAL 3.3 12.3 - - - +
183A THR* 3.5 16.8 + - + +
195A CYS 3.6 2.2 + - - +
196A GLY* 1.3 74.8 - - - -
198A LEU* 1.3 68.6 + - - +
199A GLY* 4.1 2.3 + - - -
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Residues in contact with LEU 198 (chain A).
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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72A MET* 3.4 43.5 - - + -
74A VAL* 4.0 15.3 - - + -
87A ILE* 4.3 10.1 - - + +
88A THR* 4.3 4.5 - - - -
89A GLY* 3.8 20.9 - - - +
91A LEU* 4.1 9.6 - - + -
169A THR* 3.6 39.9 - - + +
171A ALA 5.8 0.4 - - - +
181A LYS* 3.1 8.4 - - - -
182A VAL* 2.8 42.4 + - + +
196A GLY 4.3 0.4 + - - +
197A GLU* 1.3 73.8 - - - +
199A GLY* 1.3 60.5 + - - +
200A ALA 4.0 0.2 + - - -
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Residues in contact with GLY 199 (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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13A SER 5.4 0.2 - - - -
71A LYS* 4.9 9.6 - - - +
72A MET 3.0 12.3 + - - -
73A GLY* 3.4 6.2 - - - -
74A VAL* 2.7 33.4 + - - -
180A ALA 4.0 5.6 - - - -
181A LYS* 4.1 6.1 - - - -
197A GLU* 4.1 7.7 + - - -
198A LEU* 1.3 73.5 - - - +
200A ALA* 1.3 60.5 + - - -
201A ILE* 4.2 1.7 - - - +
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Residues in contact with ALA 200 (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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74A VAL 3.4 5.6 - - - -
76A TRP* 3.5 39.2 + - + +
87A ILE* 3.7 19.8 - - + +
177A TRP 5.3 0.4 - - - +
179A GLY* 5.9 1.6 + - - -
180A ALA* 3.1 23.4 + - + +
198A LEU 4.0 1.0 + - - -
199A GLY* 1.3 72.3 - - - -
201A ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 201 (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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13A SER* 3.9 26.7 - - - -
73A GLY* 3.7 17.9 - - - +
74A VAL 2.8 24.1 + - - +
75A PRO* 3.4 8.1 - - + -
76A TRP* 3.0 28.5 + - - -
199A GLY 4.2 6.7 - - - +
200A ALA* 1.3 78.5 - - - +
202A SER* 1.3 66.4 + - - +
205A SER* 3.5 15.5 - - - +
206A ALA 3.6 8.1 - - - +
208A GLN* 3.3 30.3 - - - +
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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