Contacts of the strand formed by residues 109 - 121 (chain D) in PDB entry 5AEW
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 ARG 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D ARG* 3.8 16.4 - - - +
107D PRO 4.5 10.3 + - - +
108D SER* 1.3 75.2 - - - +
110D THR* 1.3 58.4 - - - +
137D TYR* 3.8 1.9 - - - +
138D ARG* 3.5 1.2 - - - -
139D ASN* 2.6 78.4 + - + +
140D ARG* 3.5 13.0 + - - +
141D LEU 3.0 28.9 + - - +
142D GLU 5.0 2.8 + - - -
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU 4.2 3.3 + - - -
39D ASP* 2.9 41.8 + - - +
108D SER* 4.1 8.6 + - - -
109D ARG* 1.3 80.3 - - - +
111D ARG* 1.3 72.8 + - - +
112D HIS* 3.9 8.1 - - + -
136D LEU* 4.3 12.3 - - + -
137D TYR* 3.1 7.0 - - - -
138D ARG* 3.7 26.9 - - + -
186D MET* 4.8 11.4 - - + -
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLN* 6.0 1.2 - - - +
39D ASP* 3.5 30.9 + - - +
40D HIS* 4.9 12.9 + - - -
110D THR* 1.3 86.1 + - - +
112D HIS* 1.3 68.0 + - - +
113D LEU* 3.8 11.0 - - + +
135D ILE 3.5 2.3 - - - +
136D LEU* 3.3 4.5 - - - +
137D TYR* 2.9 47.0 + - + +
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Residues in contact with HIS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ALA* 3.8 31.0 - - + +
38D LEU* 3.6 29.8 - - + +
39D ASP* 2.6 36.5 + - - +
110D THR* 3.9 11.7 - - + -
111D ARG* 1.3 76.1 - - - +
113D LEU* 1.3 62.5 + - - +
114D VAL* 3.7 6.7 + - + -
134D PHE* 5.9 7.9 - + + -
135D ILE 3.8 4.0 - - - -
136D LEU* 3.2 27.3 - - + +
152D ARG* 5.6 2.9 - - - -
186D MET* 5.5 2.2 - - + -
187D PHE 2.8 27.6 + - - -
188D PHE 4.6 9.9 - - - -
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ARG* 3.8 11.0 - - + -
112D HIS* 1.3 71.4 - - - +
114D VAL* 1.3 64.8 + - - +
115D SER* 4.2 2.1 + - - -
134D PHE* 3.2 9.9 - - - +
135D ILE* 2.9 55.2 + - + +
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TYR* 4.0 34.3 - - + +
32D TYR* 4.0 28.0 + - + -
35D ALA* 4.4 7.6 - - + -
112D HIS* 3.7 14.0 + - + +
113D LEU* 1.3 80.8 - - - +
115D SER* 1.3 68.1 + - - +
117D VAL* 4.1 19.1 - - + -
132D SER* 4.5 2.2 - - - -
133D ALA 3.7 7.9 - - - +
134D PHE* 5.3 3.6 - - + -
152D ARG* 4.0 25.4 - - - +
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Residues in contact with SER 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D TYR* 5.9 0.9 - - - -
113D LEU* 4.2 3.5 + - - -
114D VAL* 1.3 77.9 - - - +
116D ASN* 1.3 84.9 + - - +
117D VAL* 3.3 7.0 + - - -
132D SER* 3.6 4.7 - - - -
133D ALA* 2.9 33.0 + - - +
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Residues in contact with ASN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D SER* 1.3 97.3 + - - +
117D VAL* 1.3 64.8 + - - +
118D ILE* 3.2 13.9 + - + +
131D ASN* 3.2 12.9 + - - +
132D SER* 3.5 3.7 - - - -
133D ALA* 3.8 22.5 - - + +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 3.0 31.6 + - - +
27D ILE* 4.0 16.8 - - + -
28D GLU* 3.8 29.5 + - + +
31D TYR* 4.0 18.4 - - + -
32D TYR* 5.5 2.2 - - + +
114D VAL* 4.1 18.8 - - + -
115D SER* 4.1 5.4 - - - +
116D ASN* 1.3 76.3 - - - +
118D ILE* 1.3 62.4 + - - +
119D VAL* 4.1 3.8 - - + -
130D VAL* 3.8 23.1 - - + -
131D ASN 3.5 4.5 - - - -
132D SER* 4.1 2.5 - - - -
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 5.1 0.7 - - - -
116D ASN* 3.8 13.2 - - + +
117D VAL* 1.3 77.3 - - - +
119D VAL* 1.3 67.9 + - - +
120D LYS* 5.5 1.7 - - + +
129D GLU 3.8 0.7 - - - +
130D VAL* 3.4 4.1 - - - -
131D ASN* 2.7 56.1 + - + +
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D SER* 5.4 1.0 + - - -
17D LYS 4.5 4.3 - - - +
19D ALA* 3.8 26.1 + - + +
23D LEU* 3.9 28.3 - - + -
24D GLN* 3.8 22.1 + - - +
27D ILE* 4.0 31.2 - - + -
117D VAL* 4.1 11.4 + - + -
118D ILE* 1.3 81.0 - - - +
120D LYS* 1.3 65.0 + - - +
121D GLU 4.3 0.2 - - - -
128D PHE* 4.2 21.3 - - + -
129D GLU 3.7 3.6 - - - +
130D VAL* 4.5 2.9 - - + +
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP* 4.6 15.4 + - - -
16D SER* 3.8 37.0 + - - +
17D LYS 5.2 2.9 - - - +
118D ILE* 5.5 2.2 - - + +
119D VAL* 1.3 77.5 - - - +
121D GLU* 1.3 76.2 + - - +
128D PHE* 3.5 4.2 - - - -
129D GLU* 2.8 68.8 + - + +
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 4.8 27.6 + - + +
18D ALA 5.3 3.3 - - - +
19D ALA* 5.3 4.7 - - + -
23D LEU* 4.2 14.2 - - + +
119D VAL* 4.3 0.6 + - - +
120D LYS* 1.3 91.5 - - - +
122D THR* 1.3 66.4 + - - +
125D PRO* 5.8 4.0 - - - +
126D ASP 5.8 1.4 + - - -
128D PHE* 3.7 30.9 - - + -
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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