Contacts of the strand formed by residues 28 - 39 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E MET* 1.3 75.5 - - - +
29E TYR* 1.3 75.0 + - - +
133E PRO* 3.8 3.3 - - - +
134E PHE* 3.3 33.8 + - - +
197E ARG 3.9 5.6 - - - -
198E CYS* 4.0 3.1 - - - -
199E ASP* 3.7 21.4 - - - +
207E CYS* 4.4 1.3 - - - -
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Residues in contact with TYR 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLY* 1.3 81.8 - - - +
30E PHE* 1.3 63.1 + - - +
131E VAL* 4.4 10.3 - - + -
132E ILE 3.0 16.6 - - - +
133E PRO* 3.2 13.9 - - + -
134E PHE* 3.2 28.0 - - - -
196E VAL* 3.3 19.8 - - - +
197E ARG* 2.4 92.3 + - - +
198E CYS 4.9 3.5 + - - -
199E ASP* 3.9 17.5 - - - -
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Residues in contact with PHE 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E TYR* 1.3 77.9 - - - +
31E GLU* 1.3 74.0 + - - +
32E LEU* 4.3 8.5 - - + -
73E VAL* 5.3 0.9 - - + -
75E LEU* 3.4 34.1 - - + -
130E VAL 4.0 0.7 - - - +
131E VAL* 3.6 4.7 - - - +
132E ILE* 2.7 50.0 + - + +
134E PHE* 4.8 1.1 - - + -
138E TRP* 3.7 20.9 - + + -
142E PHE* 4.2 20.4 - + - -
144E LEU* 4.4 13.7 - - + -
172E ILE* 4.7 2.9 - - + -
194E ILE* 3.6 38.6 - - + -
195E ARG 3.7 2.9 - - - -
196E VAL* 3.5 20.2 - - + -
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Residues in contact with GLU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E PHE* 1.3 83.0 - - - +
32E LEU* 1.3 63.9 + - - +
129E LEU* 3.1 35.5 - - + +
130E VAL 3.6 4.9 - - - +
131E VAL* 4.5 3.3 - - + +
178E TRP* 3.0 36.9 - - + -
194E ILE* 3.1 5.4 - - - -
195E ARG* 2.7 51.9 + - - +
197E ARG* 2.8 39.1 + - - +
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E PHE* 4.3 4.9 - - + -
31E GLU* 1.3 76.1 - - - +
33E GLN* 1.3 62.4 + - - +
34E LEU* 4.3 16.2 - - + +
71E VAL* 5.5 5.2 - - + -
73E VAL* 3.9 27.1 - - + -
128E GLY 3.6 1.1 - - - +
129E LEU* 3.5 5.3 - - - +
130E VAL* 2.9 46.1 + - + +
144E LEU* 3.8 39.9 - - + -
146E VAL* 4.1 10.8 - - + -
192E LEU* 4.4 17.0 - - + -
193E GLN 3.4 5.2 - - - +
194E ILE* 3.9 10.1 - - + -
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Residues in contact with GLN 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 1.3 71.0 - - - +
34E LEU* 1.3 86.0 + - - +
35E SER* 3.7 3.1 + - - -
105E LEU* 5.1 2.6 - - - +
126E ASP* 5.2 2.4 - - - +
127E PRO* 5.6 1.9 - - - +
128E GLY* 3.4 23.2 + - - +
129E LEU* 3.5 23.5 - - + +
178E TRP* 3.8 26.0 - - + -
192E LEU* 3.3 4.8 - - - -
193E GLN* 2.8 48.4 + - + +
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 4.0 10.5 - - + +
33E GLN* 1.3 89.8 + - - +
35E SER* 1.3 60.9 + - - +
36E ALA 3.6 8.7 - - - +
37E LEU* 5.1 0.2 - - + -
71E VAL* 3.7 26.2 - - + -
98E LEU* 3.6 29.2 - - + -
103E PHE* 4.3 10.8 - - + -
105E LEU* 3.6 17.7 - - + +
128E GLY* 2.8 19.8 + - - +
190E LEU* 3.4 28.5 - - + -
191E GLU 3.2 22.2 - - - +
192E LEU* 4.0 9.4 - - + -
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Residues in contact with SER 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TYR* 4.4 19.0 - - - +
33E GLN* 3.7 4.9 + - - -
34E LEU* 1.3 75.0 - - - +
36E ALA* 1.3 63.5 + - - +
104E TYR* 3.5 8.7 - - - -
105E LEU* 3.1 36.1 + - - +
191E GLU* 2.7 37.3 + - - +
192E LEU* 3.8 3.1 + - - -
193E GLN* 5.1 12.1 + - - +
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Residues in contact with ALA 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TYR* 3.8 16.6 - - + -
291A TRP* 3.7 30.7 - - + -
34E LEU* 3.6 5.3 - - - +
35E SER* 1.3 82.6 + - - +
37E LEU* 1.3 59.1 + - - +
103E PHE* 3.4 13.0 - - - +
104E TYR* 4.3 5.8 - - + -
189E HIS 4.0 1.0 - - - +
190E LEU* 3.1 8.8 - - - +
191E GLU* 3.0 28.8 + - + +
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Residues in contact with LEU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A TRP* 3.4 7.2 - - - -
34E LEU* 5.1 0.9 - - + -
36E ALA* 1.3 72.2 - - - +
38E ARG* 1.3 64.9 + - - +
39E ASN* 5.6 2.5 - - + -
69E THR* 3.5 27.8 - - + +
71E VAL* 5.5 4.3 - - + -
101E ASN 4.4 8.7 - - - +
102E SER* 3.1 1.9 - - - -
103E PHE* 2.9 68.1 + - + -
148E ALA* 4.3 12.1 - - + -
188E ALA* 4.0 22.2 - - + -
189E HIS 3.3 5.8 - - - +
190E LEU* 3.4 36.8 - - + -
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Residues in contact with ARG 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TYR* 3.5 34.8 + - - +
280A PRO* 3.6 29.7 + - - +
291A TRP* 3.6 21.8 - - + -
303A LEU* 5.3 2.4 - - - +
37E LEU* 1.3 76.9 - - - +
39E ASN* 1.3 59.4 + - - +
40E VAL* 4.3 12.7 + - + +
101E ASN 3.5 1.6 - - - -
102E SER* 3.2 17.9 - - - +
187E VAL 4.3 0.5 - - - +
188E ALA* 3.2 5.6 - - - -
189E HIS* 2.9 71.1 + - + +
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Residues in contact with ASN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 5.6 3.6 - - + -
38E ARG* 1.3 72.5 - - - +
40E VAL* 1.3 66.3 + - - +
41E ASN* 3.3 2.9 + - - +
42E GLY* 3.3 17.4 + - - -
43E GLU* 3.1 35.4 + - - +
67E CYS* 4.5 6.7 - - - +
100E GLY 5.2 0.7 - - - +
101E ASN* 2.8 41.9 + - - +
102E SER* 3.4 2.7 + - - -
163E ILE* 4.0 10.8 - - + +
187E VAL* 3.3 30.2 - - - +
188E ALA* 4.6 6.1 - - + -
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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