Contacts of the strand formed by residues 139 - 147 (chain D) in PDB entry 5LEZ
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 VAL 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ILE* 3.2 9.4 - - - +
78D MET* 5.0 1.3 - - + -
79D SER 3.6 11.9 - - - +
81D LEU 3.2 33.7 - - - +
82D ILE* 4.4 3.1 - - + +
84D ASP* 4.6 4.5 - - + -
85D ALA* 3.9 18.4 - - + +
88D LEU* 3.6 29.2 - - + -
137D PHE* 3.1 5.4 + - + +
138D GLY* 1.3 78.7 - - - +
140D ALA* 1.3 60.7 + - - +
141D LEU* 3.7 23.1 - - + -
156D MET* 4.5 4.2 - - + +
157D ASP 4.3 1.6 - - - -
158D PRO* 3.6 19.9 - - - +
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Residues in contact with ALA 140 (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 ILE* 3.6 27.3 - - + +
78D MET* 3.5 0.5 - - - +
79D SER 2.9 30.8 + - - +
139D VAL* 1.3 74.3 - - - +
141D LEU* 1.3 69.6 + - - +
155D HIS* 4.1 14.1 - - - +
156D MET 3.4 13.0 - - - +
157D ASP* 4.6 5.6 - - + -
170D ILE* 3.8 13.0 - - + +
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Residues in contact with LEU 141 (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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76D CYS* 3.9 15.0 - - - -
77D ALA 3.5 2.0 - - - -
78D MET* 3.5 23.6 - - + -
85D ALA* 4.6 6.5 - - + -
88D LEU* 4.1 30.1 - - + -
89D ILE* 4.8 4.9 - - + -
116D VAL* 4.3 2.2 - - + -
139D VAL* 3.7 15.7 - - + -
140D ALA* 1.3 83.5 - - - +
142D LEU* 1.3 62.4 + - - +
143D PHE* 3.8 34.9 - - + -
154D PHE 3.9 0.3 - - - +
155D HIS* 3.4 6.5 - - - -
156D MET* 2.8 49.2 + - + +
170D ILE* 4.5 1.3 - - - -
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Residues in contact with LEU 142 (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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37D ALA* 4.3 5.8 - - + +
38D ILE* 3.9 7.4 - - - +
39D GLY* 3.7 28.7 - - - +
48D LEU* 4.2 7.9 - - + +
75D GLY 3.9 0.3 - - - +
76D CYS* 3.2 5.4 - - - -
77D ALA* 2.8 43.5 + - + +
141D LEU* 1.3 70.3 - - - +
143D PHE* 1.3 61.3 + - - +
144D GLY 3.9 0.7 + - - -
153D LEU* 4.1 13.9 - - + -
154D PHE 3.3 5.8 - - - +
155D HIS* 3.8 31.4 - - + -
168D ARG* 3.9 26.9 - - + +
170D ILE* 3.8 26.0 - - + -
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Residues in contact with PHE 143 (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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70D ILE* 4.2 11.0 - - + -
74D ILE* 4.4 7.2 - - + -
75D GLY 3.4 3.4 - - - +
76D CYS* 3.8 23.1 - - + -
88D LEU 5.5 0.4 - - - -
89D ILE* 5.2 1.6 - - + -
92D ALA* 4.1 20.2 - - + -
109D VAL* 3.9 13.6 - - + +
112D VAL* 4.4 8.1 - - + -
113D THR* 3.6 43.7 - - + +
116D VAL* 4.0 22.4 - - + -
141D LEU* 3.8 37.9 - - + -
142D LEU* 1.3 74.7 - - - +
144D GLY* 1.3 57.7 - - - +
152D GLN 3.7 1.2 - - - +
153D LEU* 3.4 4.5 - - - +
154D PHE 2.9 35.2 + - - +
156D MET* 4.8 4.9 - - + -
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Residues in contact with GLY 144 (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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46D VAL* 3.6 23.6 - - - -
48D LEU* 4.4 6.7 - - - +
74D ILE* 3.5 3.1 - - - +
75D GLY* 2.7 42.6 + - - +
109D VAL* 4.8 0.4 - - - -
142D LEU 3.9 2.0 + - - -
143D PHE* 1.3 73.4 - - - +
145D GLY* 1.3 55.0 + - - -
152D GLN 3.4 6.7 - - - -
153D LEU* 4.2 5.1 - - - +
220D VAL* 3.8 5.3 - - - +
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Residues in contact with GLY 145 (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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46D VAL* 3.6 5.3 - - - +
73D HIS 3.1 14.6 - - - -
74D ILE* 4.1 1.1 - - - -
109D VAL* 3.8 14.6 - - - +
144D GLY* 1.3 74.4 - - - -
146D VAL* 1.3 61.5 + - - +
150D GLY 4.0 0.2 - - - +
151D PRO* 3.5 2.9 - - - +
152D GLN* 2.7 40.3 + - - +
220D VAL* 4.1 7.9 - - - -
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Residues in contact with VAL 146 (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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46D VAL* 5.2 0.2 - - + -
73D HIS* 3.0 35.4 + - + +
109D VAL* 4.1 0.8 - - - +
145D GLY* 1.3 79.7 - - - +
147D ASP* 1.3 72.5 + - - +
150D GLY* 3.6 12.3 - - - -
151D PRO* 4.0 12.1 - - + -
220D VAL* 3.7 28.0 - - + +
221D GLN* 3.7 19.3 - - - +
222D PRO* 3.9 25.4 - - + +
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Residues in contact with ASP 147 (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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73D HIS* 4.8 2.7 - - + -
106D THR* 5.4 5.2 - - - +
107D MET 4.7 4.3 - - - +
108D THR* 3.5 23.7 - - + +
109D VAL* 2.8 33.2 + - - +
110D GLU 4.5 0.5 + - - -
146D VAL* 1.3 80.6 - - - +
148D GLU* 1.3 62.6 + - - +
149D LYS* 2.9 16.3 + - - +
150D GLY* 2.8 27.1 + - - -
152D GLN* 2.9 28.3 - - - +
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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