Contacts of the strand formed by residues 28 - 39 (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 GLY 28 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C MET* 1.3 74.6 - - - +
29C TYR* 1.3 67.4 + - - +
133C PRO* 3.5 5.0 - - - +
134C PHE* 3.1 40.9 + - - +
197C ARG 3.2 14.4 - - - -
198C CYS* 4.0 1.1 - - - -
199C ASP* 3.3 15.6 + - - +
207C CYS* 4.8 0.2 - - - -
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Residues in contact with TYR 29 (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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28C GLY* 1.3 78.8 - - - +
30C PHE* 1.3 59.4 + - - +
31C GLU* 3.4 41.9 + - + +
131C VAL* 4.0 18.6 - - + -
132C ILE 3.6 5.8 - - - -
133C PRO* 3.7 14.4 - - + -
134C PHE* 3.4 8.4 - - - -
195C ARG* 4.6 3.3 + - - -
196C VAL* 3.8 1.6 - - - -
197C ARG* 2.9 67.3 + - + +
198C CYS 4.4 6.7 - - - -
199C ASP* 3.9 15.9 - - - -
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Residues in contact with PHE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TYR* 1.3 72.7 - - - +
31C GLU* 1.3 70.2 + - - +
32C LEU* 4.3 16.2 - - + -
73C VAL* 5.1 2.9 - - + -
75C LEU* 3.6 41.1 - - + -
130C VAL 3.8 0.7 - - - +
131C VAL* 3.4 2.6 - - - -
132C ILE* 2.7 54.4 + - + +
134C PHE* 3.8 8.5 - - + -
138C TRP* 3.7 15.5 - + - -
142C PHE* 4.4 12.1 - + - -
144C LEU* 4.7 7.6 - - + -
172C ILE* 4.8 1.6 - - + -
194C ILE* 3.9 30.5 - - + -
195C ARG 3.9 7.0 - - - -
196C VAL* 3.6 25.1 - - + +
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Residues in contact with GLU 31 (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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29C TYR* 3.4 35.5 + - + +
30C PHE* 1.3 78.0 - - - +
32C LEU* 1.3 61.6 + - - +
129C LEU* 4.4 13.1 - - + +
130C VAL 3.5 2.7 - - - -
131C VAL* 3.9 23.0 - - + +
178C TRP* 4.0 17.7 - - + -
194C ILE* 3.4 6.5 - - - +
195C ARG* 2.8 76.7 + - + +
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Residues in contact with LEU 32 (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* 4.3 7.4 - - + -
31C GLU* 1.3 77.2 - - - +
33C GLN* 1.3 63.7 + - - +
34C LEU* 4.3 15.0 - - + +
71C VAL* 5.7 2.9 - - + -
73C VAL* 4.0 32.3 - - + -
128C GLY 3.7 1.9 - - - +
129C LEU* 3.4 4.6 - - - +
130C VAL* 2.9 45.5 + - + +
144C LEU* 3.9 25.4 - - + -
146C VAL* 4.3 6.7 - - + -
178C TRP* 4.7 0.2 - - - -
192C LEU* 4.1 17.7 - - + -
193C GLN 3.3 11.4 - - - +
194C ILE* 3.8 17.3 - - + -
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Residues in contact with GLN 33 (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* 1.3 73.2 - - - +
34C LEU* 1.3 87.9 + - - +
35C SER* 3.8 5.3 + - - +
105C LEU* 4.6 5.3 - - - +
106C PRO 5.5 4.0 + - - -
107C PRO* 6.1 5.5 - - + +
126C ASP* 4.5 11.1 - - - +
127C PRO* 5.9 0.8 - - - +
128C GLY* 3.6 15.0 + - - +
129C LEU* 3.4 27.0 + - + +
178C TRP* 4.1 21.7 - - + -
192C LEU* 3.2 6.7 - - - -
193C GLN* 2.8 48.5 + - - +
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Residues in contact with LEU 34 (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* 4.1 8.9 - - + +
33C GLN* 1.3 96.1 + - - +
35C SER* 1.3 60.3 + - - +
36C ALA 3.3 29.2 - - - +
37C LEU* 4.9 3.6 - - + -
71C VAL* 3.7 33.7 - - + -
95C THR* 6.2 0.4 - - + -
98C LEU* 4.5 10.1 - - + -
103C PHE* 4.0 23.8 - - + -
105C LEU* 3.3 15.8 - - + +
128C GLY* 2.9 15.8 + - - +
190C LEU* 4.5 15.3 - - + -
191C GLU 3.4 13.5 - - - +
192C LEU* 4.0 10.8 - - + -
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Residues in contact with SER 35 (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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266B TYR* 4.3 17.0 - - - +
33C GLN* 3.8 6.9 + - - +
34C LEU* 1.3 75.7 - - - +
36C ALA* 1.3 63.1 + - - +
104C TYR* 3.6 6.9 - - - -
105C LEU* 3.0 40.9 + - - +
107C PRO* 5.8 8.1 - - - -
191C GLU* 2.9 32.2 + - - +
192C LEU* 4.1 2.0 + - - -
193C GLN* 5.8 6.5 + - - +
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Residues in contact with ALA 36 (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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266B TYR* 3.6 31.6 - - + -
291B TRP* 3.7 16.8 - - + -
34C LEU* 3.3 15.2 - - - +
35C SER* 1.3 80.7 - - - +
37C LEU* 1.3 61.2 + - - +
103C PHE* 3.6 9.9 - - - +
104C TYR* 4.3 4.9 - - + -
190C LEU* 3.5 1.4 - - - -
191C GLU* 3.1 30.7 + - + -
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Residues in contact with LEU 37 (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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291B TRP* 3.2 8.7 - - - -
34C LEU* 4.9 5.8 - - + -
36C ALA* 1.3 76.8 - - - +
38C ARG* 1.3 69.1 + - - +
39C ASN* 4.5 2.5 - - + -
69C THR* 4.2 10.5 - - + +
71C VAL* 5.1 3.6 - - + -
101C ASN 3.8 17.3 - - - +
102C SER* 3.3 1.0 - - - -
103C PHE* 3.0 63.9 + - + -
148C ALA* 4.1 20.6 - - + -
163C ILE* 5.7 2.5 - - + -
188C ALA* 4.3 11.7 - - + -
189C HIS 3.3 12.6 - - - +
190C LEU* 3.6 27.1 - - + -
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Residues in contact with ARG 38 (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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279B TYR* 3.2 42.5 - - - +
280B PRO* 3.8 36.8 + - - +
291B TRP* 3.6 16.5 - - + -
37C LEU* 1.3 77.1 - - - +
39C ASN* 1.3 59.9 + - - +
40C VAL* 4.4 18.9 - - + +
101C ASN 4.0 0.4 - - - -
102C SER* 3.3 4.3 - - - -
187C VAL 4.2 0.9 - - - +
188C ALA* 3.1 7.6 - - - +
189C HIS* 3.0 76.6 + - + +
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Residues in contact with ASN 39 (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* 4.5 3.1 - - + -
38C ARG* 1.3 72.2 - - - +
40C VAL* 1.3 69.0 + - - +
41C ASN 4.2 1.6 + - - -
42C GLY* 3.3 8.8 + - - -
43C GLU* 3.1 42.4 + - - +
67C CYS* 3.8 11.3 - - - -
101C ASN* 3.2 32.8 + - - +
102C SER* 2.9 12.5 + - - -
163C ILE* 3.8 11.1 - - + +
187C VAL* 3.3 27.4 - - - +
188C ALA* 4.4 7.6 - - + -
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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