Contacts of the strand formed by residues 130 - 139 (chain D) in PDB entry 4QAE
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 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.5 25.6 - - + -
40D GLU* 2.7 41.9 + - - -
126D VAL* 3.4 5.5 - - - +
127D TRP* 2.8 65.6 + - - +
128D GLN* 3.9 19.6 + - - +
129D ASN* 1.3 79.6 - - - +
131D GLU* 1.3 66.8 + - - +
132D VAL* 4.0 6.2 + - + +
13S CYS 3.1 20.4 + - - -
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Residues in contact with GLU 131 (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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7D LEU* 6.0 1.6 - - - +
8D ILE 4.8 1.0 - - - +
9D PRO* 5.7 0.7 - - - +
10D ALA* 3.3 37.3 + - + +
39D ASN* 3.1 18.4 + - - -
40D GLU* 5.0 0.7 - - - +
124D LYS* 2.7 34.2 + - + +
125D VAL 3.5 5.8 - - - +
126D VAL* 4.6 13.1 - - + +
130D ARG* 1.3 81.6 - - - +
132D VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 132 (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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39D ASN* 3.5 11.4 - - - +
40D GLU* 3.4 37.7 - - + +
124D LYS* 3.3 2.5 - - - +
125D VAL* 2.9 34.6 + - + +
127D TRP* 4.3 10.3 - - + -
130D ARG* 4.0 9.9 - - + +
131D GLU* 1.3 76.3 - - - +
133D PHE* 1.3 64.6 + - - +
134D TRP* 4.0 3.0 - - + -
10S CYS* 3.8 11.7 - - - -
11S CYS 3.6 23.6 - - - +
13S CYS* 3.9 20.0 - - - +
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Residues in contact with PHE 133 (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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8D ILE* 4.2 1.6 - - + -
9D PRO 3.4 20.9 - - - -
10D ALA* 3.6 17.7 - - + -
11D PRO* 4.0 9.0 - - + -
38D GLY* 3.1 19.9 - - - -
39D ASN* 2.9 40.8 + - + +
40D GLU 4.6 0.5 + - - -
122D PHE* 3.6 29.4 - + + -
123D PHE 3.1 14.1 - - - +
124D LYS* 4.0 6.5 - - + -
132D VAL* 1.3 76.2 - - - +
134D TRP* 1.3 72.8 + - - +
159D LEU* 3.9 27.8 - - + -
161D LEU* 3.7 39.7 - - + -
11S CYS 4.9 0.7 - - - +
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Residues in contact with TRP 134 (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 LEU* 3.6 27.1 - - + -
37D ALA 3.1 13.5 - - - +
38D GLY* 3.9 4.9 - - - -
41D VAL* 5.0 0.4 - - + -
52D TRP* 4.9 1.6 - - - -
81D GLN* 6.2 0.2 - - - -
122D PHE* 3.5 2.8 - - - -
123D PHE* 2.7 79.1 + + + +
125D VAL* 3.8 16.4 - - + -
132D VAL* 4.0 13.2 - - + -
133D PHE* 1.3 86.5 - - - +
135D VAL* 1.3 61.9 + - - +
136D THR* 4.2 6.7 - - + +
9S PHE* 3.6 27.0 - + - -
10S CYS* 3.5 29.4 - - - -
11S CYS* 3.7 46.2 - - + +
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Residues in contact with VAL 135 (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 LEU* 3.4 5.7 - - - +
37D ALA* 2.7 38.7 + - + +
120D MET* 4.6 2.7 - - + -
121D VAL 3.2 15.5 - - - +
122D PHE* 4.1 11.4 - - + -
133D PHE* 5.0 3.1 - - + -
134D TRP* 1.3 79.3 - - - +
136D THR* 1.3 69.3 + - - +
152D PHE* 3.6 26.4 - - + -
155D PHE* 4.0 22.7 - - + -
156D SER* 4.8 3.4 - - - +
159D LEU* 3.8 28.9 - - + -
161D LEU* 5.2 2.5 - - + -
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Residues in contact with THR 136 (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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33D VAL* 4.2 10.3 - - + -
35D GLY 3.3 5.2 - - - -
36D LEU* 4.0 17.5 - - + -
52D TRP* 4.5 9.6 - - + -
119D ALA 3.7 0.3 - - - +
120D MET* 3.2 6.8 - - - -
121D VAL* 2.9 30.6 + - - +
123D PHE* 3.4 29.3 - - + -
134D TRP* 4.2 5.2 - - + -
135D VAL* 1.3 80.7 - - - +
137D LEU* 1.3 59.3 + - - +
138D TYR* 3.5 30.7 - - + +
152D PHE* 4.2 0.2 - - - -
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Residues in contact with LEU 137 (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 3.7 0.2 - - - +
33D VAL* 3.7 1.7 - - - -
34D VAL* 2.8 40.4 + - + -
35D GLY 2.8 18.8 + - - +
118D HIS* 4.9 7.0 - - + +
119D ALA 3.4 15.7 - - - +
120D MET* 3.9 14.1 - - + -
136D THR* 1.3 71.0 - - - +
138D TYR* 1.3 55.4 + - - +
144D LEU* 3.8 28.3 - - + -
148D LEU* 4.2 14.8 - - + +
149D LYS* 4.1 27.4 - - + +
152D PHE* 3.8 37.1 - - + -
168D PHE* 4.5 1.6 - - + -
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Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D PHE* 4.1 6.3 - + - -
31D TRP* 3.4 35.7 - + + -
32D TYR 3.2 9.9 - - - -
33D VAL* 3.9 19.3 - - + -
54D THR* 3.8 18.3 + - - +
56D TYR* 2.8 41.3 + + - -
118D HIS* 3.2 6.1 - - - -
119D ALA* 2.7 36.4 + - + +
121D VAL* 3.6 27.6 - - + -
123D PHE* 3.5 13.3 - - - -
136D THR* 3.5 27.2 - - + +
137D LEU* 1.3 73.7 - - - +
139D GLY* 1.3 57.4 + - - +
144D LEU* 3.5 9.5 - - - +
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Residues in contact with GLY 139 (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 TRP* 3.6 7.4 - - - -
32D TYR* 2.8 39.3 + - - -
34D VAL* 3.9 3.7 - - - +
117D GLN 3.4 7.2 - - - -
138D TYR* 1.3 73.7 - - - +
140D ARG* 1.3 67.0 + - - -
141D THR 3.2 14.0 + - - +
144D LEU* 3.9 12.8 - - - -
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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