Contacts of the strand formed by residues 114 - 126 (chain D) in PDB entry 3ALQ
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 TRP 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D PHE* 3.7 12.3 - - + -
65D SER* 3.1 28.8 - - - -
66D GLY* 3.0 51.5 + - - +
68D GLY 3.0 28.7 + - - -
69D CYS* 4.1 15.0 - - - -
74D VAL* 4.9 4.9 - - + -
76D LEU* 3.9 10.5 - - + -
100D PRO* 3.7 32.8 - - + +
101D CYS* 3.9 5.7 - - - -
112D ASN 4.4 3.6 - - - -
113D PRO* 1.3 73.0 - - - +
115D TYR* 1.3 68.5 + - - +
116D GLU* 3.8 15.0 - - + -
141D TYR* 3.7 29.6 - + - -
98E ARG* 5.8 0.4 - - - +
99E SER* 3.1 10.5 - - - +
102E GLN* 3.7 17.0 - - - +
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Residues in contact with TYR 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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63D LEU* 4.6 5.6 - - + -
64D PHE 3.4 4.7 - - - +
65D SER* 3.5 24.2 + - - -
113D PRO* 4.0 20.5 - - + +
114D TRP* 1.3 79.1 - - - +
116D GLU* 1.3 59.3 + - - +
117D PRO* 3.8 4.9 - - - +
143D ASP* 3.7 11.8 + - - -
75E LEU* 4.1 29.4 - - + -
97E ILE* 3.6 40.8 - - + +
98E ARG* 2.7 36.1 + - - +
99E SER* 2.9 6.8 + - - +
106U LEU* 5.1 1.3 - - + -
113U ARG* 3.8 29.9 + - - -
114U LEU* 4.2 21.4 - - + +
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Residues in contact with GLU 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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63D LEU* 3.3 4.9 - - - +
64D PHE* 2.7 48.1 + - + +
76D LEU* 4.0 15.7 - - + -
98D ARG* 3.0 57.6 + - + +
100D PRO* 3.7 37.0 - - + +
114D TRP* 3.8 5.6 - - + -
115D TYR* 1.3 78.9 - - - +
117D PRO* 1.3 66.8 - - - +
98E ARG* 3.3 20.4 + - - -
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Residues in contact with PRO 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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61D GLN* 5.1 6.5 - - - +
62D VAL 3.4 8.5 - - - +
63D LEU* 3.7 9.0 - - + -
98D ARG* 4.7 4.7 - - - +
116D GLU* 1.3 91.7 - - - +
118D ILE* 1.3 70.1 + - - +
96E ALA* 4.3 19.3 - - + -
97E ILE 3.3 25.4 - - - +
98E ARG* 3.7 22.7 - - + +
117E PRO 5.8 1.1 - - - +
118E ILE* 5.1 8.7 - - + -
119E TYR 6.0 1.3 - - - +
117F PRO* 5.9 0.3 - - - +
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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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61D GLN* 3.3 6.6 - - - +
62D VAL* 3.0 38.2 + - + -
64D PHE* 4.3 14.8 - - + -
76D LEU 3.9 14.1 - - - +
78D HIS* 3.8 26.4 - - + -
96D ALA* 3.8 32.5 - - + +
97D ILE 4.2 3.6 - - - +
98D ARG* 3.7 29.2 - - + -
116D GLU 5.0 0.9 - - - +
117D PRO* 1.3 84.5 - - - +
119D TYR* 1.3 62.3 + - - +
120D LEU* 3.9 7.6 - - + -
117F PRO* 5.0 7.2 - - + -
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Residues in contact with TYR 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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59D TYR* 3.2 20.9 - - + +
60D SER 3.4 7.6 - - - -
61D GLN* 4.0 6.1 - - + -
96D ALA* 5.4 0.2 - - - +
118D ILE* 1.3 76.2 - - - +
120D LEU* 1.3 90.6 + - - +
121D GLY* 4.1 0.4 - - - -
151D TYR* 3.4 22.4 - + - -
57E LEU* 5.9 1.2 - - - +
119E TYR* 3.8 37.5 + + + +
121E GLY* 2.9 42.2 + - - -
61F GLN* 3.3 10.4 - - - +
119F TYR* 3.9 44.4 - + + +
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Residues in contact with LEU 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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59D TYR* 2.9 3.1 - - - -
60D SER 2.7 35.7 + - - +
78D HIS* 3.4 44.6 - - + +
80D ILE* 3.8 17.3 - - + +
94D LEU* 3.5 35.7 - - + +
95D SER 4.1 5.8 - - - +
96D ALA* 3.7 22.9 - - + -
118D ILE* 3.9 4.7 - - + -
119D TYR* 1.3 96.3 - - - +
121D GLY* 1.3 59.2 + - - +
61F GLN* 3.5 14.6 - - - +
119F TYR* 4.7 0.2 - - - -
151F TYR* 3.9 3.1 - - - -
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Residues in contact with GLY 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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57D LEU* 4.7 3.6 - - - -
58D ILE 2.8 13.0 - - - -
59D TYR* 3.8 6.5 - - - -
94D LEU* 3.6 8.5 - - - +
119D TYR* 4.2 1.1 - - - -
120D LEU* 1.3 76.6 - - - +
122D GLY* 1.3 56.8 + - - -
59F TYR* 3.5 3.0 - - - -
119F TYR* 2.7 27.6 + - - -
151F TYR* 3.2 23.9 + - - -
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Residues in contact with GLY 122 (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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57D LEU* 3.8 10.8 - - - +
58D ILE 2.8 27.5 + - - -
94D LEU* 3.9 5.1 - - - +
121D GLY* 1.3 73.3 - - - -
123D VAL* 1.3 59.8 + - - -
124D PHE* 3.1 21.6 - - - -
15F HIS* 4.5 1.1 - - - -
59F TYR* 3.3 19.1 - - - -
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Residues in contact with VAL 123 (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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55D LEU* 4.0 16.2 - - + +
56D TYR 3.2 11.4 - - - +
57D LEU* 4.6 7.9 - - + -
122D GLY* 1.3 70.8 - - - -
124D PHE* 1.3 70.2 + - - +
157D LEU* 4.6 7.9 - - + -
13F VAL* 4.1 13.5 - - + -
14F ALA 5.5 0.2 - - - +
15F HIS* 3.5 23.1 - - + +
34F ASN 5.3 0.2 - - - +
36F LEU* 3.6 7.0 - - + +
57F LEU* 4.9 1.6 - - + -
59F TYR* 2.7 33.4 + - + +
154F ILE 5.0 0.9 - - - +
155F ILE* 3.9 45.8 - - + -
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Residues in contact with PHE 124 (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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55D LEU* 4.3 1.3 - - - -
56D TYR 2.7 38.4 + - - +
58D ILE* 3.8 26.9 - - + -
93D LEU* 3.4 57.2 - - + -
94D LEU* 3.8 17.3 - - + -
122D GLY* 3.1 39.3 - - - -
123D VAL* 1.3 74.5 - - - +
125D GLN* 1.3 62.0 + - - +
126D LEU* 3.4 15.6 + - + +
15F HIS* 3.7 18.4 - - - -
34F ASN* 3.8 31.2 - - + +
36F LEU* 4.2 3.1 - - - -
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Residues in contact with GLN 125 (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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53D GLU* 3.7 32.9 + - - +
54D GLY* 3.4 11.5 - - - +
55D LEU* 3.6 24.4 - - + +
82D ARG* 3.9 14.4 + - - -
124D PHE* 1.3 70.1 - - - +
126D LEU* 1.3 72.3 + - - +
127D GLU* 4.5 9.3 + - + -
9F SER 5.6 2.8 + - - -
34F ASN* 5.1 3.5 - - - +
36F LEU* 3.7 22.0 - - + +
69W PRO* 5.8 8.1 - - + -
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Residues in contact with LEU 126 (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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50D VAL* 3.9 23.1 - - + -
52D SER 4.8 0.7 - - - -
53D GLU* 3.3 8.5 - - - +
54D GLY 2.8 32.9 + - - -
56D TYR* 3.5 41.3 - - + -
58D ILE* 3.9 17.0 - - + -
82D ARG* 3.4 35.0 - - + +
93D LEU* 4.8 0.2 - - + -
124D PHE* 3.6 20.4 - - + +
125D GLN* 1.3 81.8 + - - +
127D GLU* 1.3 65.1 + - - +
130D ASP* 3.8 5.4 - - + +
132D LEU* 3.9 10.1 - - + -
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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