Contacts of the strand formed by residues 163 - 172 (chain C) in PDB entry 1DVM
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 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C LEU* 5.3 3.8 - - + -
49C THR* 5.9 0.4 - - - +
97C ILE* 3.8 28.9 - - + -
98C PHE 3.2 12.3 - - - +
99C VAL* 4.1 8.3 - - + -
161C THR* 3.9 1.8 - - - +
162C ARG* 1.3 80.9 - - - +
164C VAL* 1.3 64.0 + - - +
306C PHE* 4.0 26.2 - - + -
309C LEU* 4.0 22.2 - - + -
315C LEU* 4.6 8.7 - - + -
316C HIS 3.6 26.0 + - - +
317C VAL* 3.9 23.0 - - + -
318C ALA* 2.9 34.4 + - - +
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA 4.6 0.4 - - - -
97C ILE* 3.5 11.5 - - - +
98C PHE* 2.8 43.9 + - + +
126C PHE* 3.9 12.3 - - + -
136C ILE* 4.8 6.5 - - + -
154C THR* 6.5 0.4 - - + -
157C VAL* 4.2 8.1 - - + -
161C THR* 3.7 23.6 - - + -
163C LEU* 1.3 82.5 - - - +
165C LEU* 1.3 80.0 + - - +
166C VAL* 4.0 13.5 - - + -
317C VAL* 5.3 2.0 - - - -
319C LEU* 3.5 36.1 - - + +
321C LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 3.6 40.2 - - + +
43C LEU* 4.2 15.9 - - + -
46C LEU* 3.7 38.8 - - + -
96C ALA 3.7 5.4 - - - +
97C ILE* 4.9 5.6 - - + +
164C VAL* 1.3 75.5 - - - +
166C VAL* 1.3 75.1 + - - +
286C LEU* 4.6 10.3 - - + -
298C MET* 5.1 2.2 - - + -
317C VAL* 4.8 7.0 - - + -
319C LEU 2.9 14.4 + - - +
320C ALA* 4.3 12.3 - - + -
321C LEU* 2.9 31.2 + - - +
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 3.6 9.0 - - - +
94C THR* 4.6 3.1 - - + +
95C ASP* 3.7 1.0 - - - -
96C ALA* 3.1 34.5 + - + +
98C PHE* 4.3 9.4 - - + -
136C ILE* 4.2 13.2 - - + -
140C VAL* 3.9 15.0 - - + -
151C LEU* 3.2 39.5 - - + -
154C THR* 5.8 0.7 - - + -
164C VAL* 4.0 15.3 - - + -
165C LEU* 1.3 83.8 - - - +
167C ASN* 1.3 74.3 + - - +
168C ALA 4.5 0.4 - - - +
321C LEU* 3.5 11.9 - - + +
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Residues in contact with ASN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLY* 3.1 23.0 - - - -
42C VAL* 4.1 12.1 - - + -
94C THR 3.4 8.3 + - - -
95C ASP* 2.7 28.5 + - - -
151C LEU* 4.9 0.2 - - - +
165C LEU* 5.0 0.2 - - + -
166C VAL* 1.3 79.0 - - - +
168C ALA* 1.3 55.2 + - - +
169C LEU* 3.4 19.2 - - - +
286C LEU* 5.5 0.9 - - + -
321C LEU 2.9 9.3 + - - +
322C GLN* 2.9 42.8 + - + +
323C LYS* 2.6 32.7 + - - +
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Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C THR* 3.5 2.3 - - - -
94C THR* 3.0 41.2 + - + +
140C VAL* 3.3 37.2 - - + -
144C THR* 3.9 8.0 - - + +
148C ILE* 4.4 7.2 - - + -
151C LEU* 5.0 0.7 - - + -
166C VAL* 4.8 1.1 - - + -
167C ASN* 1.3 76.0 - - - +
169C LEU* 1.3 63.0 + - - +
323C LYS* 3.2 11.4 - - + +
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 3.0 31.0 - - - +
37C TYR* 5.1 8.1 - - + -
38C GLY* 4.7 5.4 - - - -
91C ILE* 4.8 0.2 - - + -
92C SER 3.4 3.6 - - - -
93C THR* 3.5 32.1 - - + -
94C THR 4.3 0.2 - - - +
144C THR* 5.0 0.7 - - - -
148C ILE* 3.1 19.6 - - - +
167C ASN* 3.4 30.1 - - - +
168C ALA* 1.3 88.9 - - - +
170C TYR* 1.3 61.0 + - - +
323C LYS 2.9 6.7 + - - +
324C VAL* 4.1 8.1 - - + -
325C LYS 3.2 13.2 + - - -
371C LEU* 4.7 2.5 - - + +
372C PHE* 3.4 26.9 - - + -
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Residues in contact with TYR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASP 5.2 3.8 - - - -
90C GLU 3.9 7.4 - - - -
91C ILE* 3.3 10.4 - - - +
92C SER* 2.7 50.5 + - - +
144C THR* 4.8 6.1 - - - +
145C LYS* 6.1 0.2 - - + -
147C MET* 3.8 45.4 - - + -
148C ILE* 4.9 1.8 - - + -
169C LEU* 1.3 76.0 - - - +
171C PHE* 1.3 66.7 - - - +
172C ASN* 3.2 42.7 + - + +
325C LYS* 3.5 32.8 - - + -
327C GLU* 3.0 29.8 + - - -
372C PHE* 4.3 0.9 - - - -
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Residues in contact with PHE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 3.3 26.2 - - + -
91C ILE* 3.9 17.5 - - + -
170C TYR* 1.3 83.1 - - - +
172C ASN* 1.3 61.1 + - - +
173C GLY 4.2 6.7 - - - -
228C TYR* 3.5 42.8 - + - -
233C LEU* 3.8 20.0 - - + -
325C LYS 3.1 8.5 + - - +
326C ILE* 3.5 24.2 - - + +
327C GLU 3.0 23.9 + - - +
362C VAL* 3.5 28.7 - - + -
372C PHE* 3.5 25.1 - + + -
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Residues in contact with ASN 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASP 4.7 7.6 - - - +
90C GLU* 3.1 28.2 + - - +
170C TYR* 3.2 28.3 + - + +
171C PHE* 1.3 72.3 - - - +
173C GLY* 1.3 73.6 + - - +
174C GLN* 4.1 1.9 + - - +
327C GLU* 3.1 29.4 + - - +
329C ASN* 4.4 14.7 + - - +
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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