Contacts of the strand formed by residues 141 - 150 (chain C) in PDB entry 5MWF
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 SER 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C TYR* 3.8 26.0 + - - +
90C TYR* 4.2 6.9 + - - -
138C TRP* 5.2 0.2 - - - -
139C PRO* 2.6 36.5 + - - +
140C ARG* 1.3 73.3 + - - +
142C PHE* 1.3 64.7 + - - +
170C GLY 3.5 7.9 - - - -
171C MET* 4.3 6.7 - - - +
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Residues in contact with PHE 142 (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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30C PHE* 4.4 4.9 - + - -
75C LEU* 3.6 21.5 - - + -
76C LYS 3.7 11.2 - - - +
78C TYR* 3.5 17.4 - - - +
90C TYR* 4.4 3.1 - - + -
138C TRP* 4.2 16.2 - + + -
140C ARG 3.7 11.0 - - - -
141C SER* 1.3 75.1 - - - +
143C THR* 1.3 67.6 + - - +
144C LEU* 3.8 21.5 - - + -
168C HIS* 4.2 17.7 - + - -
170C GLY* 3.0 45.1 + - - +
171C MET 3.9 1.1 - - - -
172C ILE* 3.4 32.3 - - + -
194C ILE* 3.6 28.9 - - + -
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Residues in contact with THR 143 (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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74C CYS 3.8 1.2 - - - +
75C LEU* 3.6 6.2 - - - +
76C LYS* 3.0 49.6 + - - +
77C GLU 2.8 24.2 + - - -
78C TYR* 3.2 0.9 - - - -
79C GLN* 3.0 23.6 + - + +
82C VAL* 3.9 28.3 - - + -
142C PHE* 1.3 75.2 + - - +
144C LEU* 1.3 68.1 + - - +
145C ILE* 4.4 1.1 - - + -
168C HIS 3.5 6.7 - - - +
169C ALA* 4.0 6.6 - - + +
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Residues in contact with LEU 144 (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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30C PHE* 4.7 3.8 - - + -
32C LEU* 3.9 20.6 - - + -
73C VAL* 3.6 30.7 - - + -
74C CYS 3.7 4.5 - - - +
75C LEU* 4.5 10.3 - - + -
142C PHE* 3.8 14.3 - - + -
143C THR* 1.3 73.9 - - - +
145C ILE* 1.3 70.6 + - - +
146C VAL* 3.8 16.6 - - + -
167C SER* 3.2 4.4 - - - -
168C HIS* 2.7 43.0 + - + +
181C LEU* 4.2 17.3 - - + -
183C PHE* 5.0 4.3 - - + -
192C LEU* 4.7 1.6 - - + -
194C ILE* 4.2 19.5 - - + -
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Residues in contact with ILE 145 (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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72C ARG 3.9 0.5 - - - +
73C VAL* 3.5 3.1 - - - -
74C CYS* 2.8 53.4 + - + +
76C LYS* 3.9 18.6 - - - +
82C VAL* 4.4 4.3 - - + -
83C THR 3.4 26.0 - - - +
84C PRO* 3.6 16.2 - - + +
85C THR* 5.3 0.2 - - - -
143C THR* 4.4 7.2 - - + -
144C LEU* 1.3 80.6 - - - +
146C VAL* 1.3 66.7 + - - +
147C GLU* 4.7 7.7 - - - +
165C ARG* 4.1 24.7 - - + +
166C VAL 3.4 9.2 - - - +
167C SER* 4.2 11.0 - - - -
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Residues in contact with VAL 146 (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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32C LEU* 4.3 11.0 - - + -
71C VAL* 3.7 26.2 - - + -
72C ARG 3.5 4.3 - - - +
73C VAL* 4.5 5.2 - - + -
144C LEU* 3.8 29.6 - - + -
145C ILE* 1.3 79.1 - - - +
147C GLU* 1.3 63.4 + - - +
164C GLU 4.2 0.3 - - - +
165C ARG* 3.6 1.0 - - - -
166C VAL* 2.8 47.6 + - + +
183C PHE* 5.3 2.9 - - + -
190C LEU* 4.5 13.7 - - + -
192C LEU* 4.4 20.6 - - + -
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Residues in contact with GLU 147 (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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70C TYR 3.9 0.2 - - - +
71C VAL* 3.4 8.9 - - - +
72C ARG* 2.4 78.4 + - + +
74C CYS* 5.9 4.5 - - - +
84C PRO 5.5 0.2 - - - +
145C ILE* 4.7 7.7 - - + +
146C VAL* 1.3 77.8 - - - +
148C ALA* 1.3 60.7 + - - +
149C TRP* 3.4 16.9 + - - +
162C LEU* 3.6 10.8 - - + -
164C GLU 3.1 11.4 - - - +
165C ARG* 3.3 34.8 + - + +
190C LEU* 5.9 1.6 - - - -
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Residues in contact with ALA 148 (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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37C LEU* 4.1 26.0 - - + -
69C THR* 4.3 6.3 - - + -
70C TYR 3.4 6.7 - - - +
71C VAL* 5.4 1.3 - - + -
147C GLU* 1.3 73.8 - - - +
149C TRP* 1.3 56.6 + - - +
162C LEU* 3.2 7.1 - - - +
163C ILE* 2.5 47.9 + - + -
164C GLU* 2.8 18.6 + - + +
190C LEU* 5.2 4.9 - - + +
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Residues in contact with TRP 149 (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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69C THR* 3.3 5.2 - - - -
70C TYR* 2.9 65.7 + - + +
72C ARG* 4.0 23.5 - - + +
147C GLU* 3.4 42.6 + - + +
148C ALA* 1.3 80.1 - - - +
150C ASP* 1.3 59.0 + - - +
158C ASN 3.4 22.9 - - - -
159C GLU* 3.6 31.9 - - - -
161C LEU* 3.3 26.2 - - + -
162C LEU* 3.4 35.7 - - + +
163C ILE* 3.6 5.2 - - - -
165C ARG* 4.6 5.6 - - - -
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Residues in contact with ASP 150 (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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44C LEU* 4.0 6.0 - - + +
50C CYS* 3.5 33.8 - - - +
51C ASP* 3.5 0.9 - - - +
67C CYS* 3.9 0.7 - - + -
68C ASP 3.1 15.8 + - - -
70C TYR* 3.8 6.7 + - - -
149C TRP* 1.3 72.7 - - - +
151C TRP* 1.3 68.7 + - - +
152C ASP* 3.0 3.2 - - - +
161C LEU* 2.9 42.9 + - + +
163C ILE* 3.5 6.4 - - + +
406C CA 2.5 22.6 - - - -
407C CA 2.5 29.3 - - - -
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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