Contacts of the strand formed by residues 144 - 157 (chain A) in PDB entry 5LLK
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 HIS 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ILE* 4.2 13.7 - - + -
95A LYS* 3.1 38.7 + - - +
136A THR* 3.4 18.1 + - + +
137A ARG 3.8 3.1 - - - -
138A LEU* 3.6 26.7 - - + +
142A GLY 3.9 6.7 - - - -
143A SER* 1.3 71.6 - - - +
145A ILE* 1.3 63.1 + - - +
146A PRO* 3.5 8.5 - - - +
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Residues in contact with ILE 145 (chain A).
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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136A THR* 3.2 2.9 - - - -
137A ARG* 2.8 34.9 + - + +
138A LEU 4.7 0.9 - - - -
139A GLY* 3.9 25.1 - - - +
143A SER* 4.2 10.1 - - - +
144A HIS* 1.3 71.7 - - - +
146A PRO* 1.3 71.3 - - + +
147A GLN* 2.9 29.9 - - - +
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Residues in contact with PRO 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA 4.0 0.4 - - - +
136A THR* 4.0 15.9 - - + -
144A HIS 3.5 8.9 - - - +
145A ILE* 1.3 92.7 - - + +
147A GLN* 1.3 64.5 + - - +
148A THR 5.5 0.7 - - - +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASP* 4.3 3.8 - - - +
135A ALA* 2.8 26.8 + - + +
136A THR* 3.8 8.5 - - - -
137A ARG* 3.4 54.3 - - + +
145A ILE* 2.9 39.6 - - - +
146A PRO* 1.3 76.3 - - - +
148A THR* 1.3 63.5 + - + +
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR 4.2 16.1 + - - +
64A VAL* 5.2 4.5 - - - +
65A VAL 5.6 0.7 + - - -
87A ILE* 3.6 39.7 - - + +
134A SER* 3.3 4.0 - - - -
135A ALA* 3.0 31.7 + - + +
146A PRO* 5.5 0.5 - - - +
147A GLN* 1.3 80.4 - - + +
149A SER* 1.3 72.5 + - - +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ILE* 6.1 0.2 - - - -
132A SER* 3.2 22.3 + - - -
133A VAL 3.3 6.1 - - - -
134A SER* 3.5 8.4 + - - -
148A THR* 1.3 84.3 + - - +
150A SER* 1.3 61.2 + - - +
151A VAL* 4.2 9.2 - - - +
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 2.2 34.1 + - - -
66A GLY* 3.9 6.1 - - - -
67A ILE* 3.9 24.0 + - - +
87A ILE* 4.5 10.5 - - - -
131A ILE 3.8 0.9 - - - +
132A SER* 3.6 0.3 - - - -
133A VAL* 2.8 37.5 + - - +
149A SER* 1.3 74.9 + - - +
151A VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 4.6 5.3 + - - +
99A ALA* 4.4 8.1 - - + -
130A TYR* 4.2 22.4 - - + -
131A ILE 3.2 14.1 - - - +
132A SER* 3.9 21.5 - - - +
149A SER* 4.2 7.2 - - - +
150A SER* 1.3 82.1 + - - +
152A PHE* 1.3 71.3 + - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 3.4 53.8 - - + +
68A PRO 3.6 14.1 - - - +
69A ASP* 3.5 9.0 - - - +
70A GLY* 4.8 1.6 - - - -
78A PHE* 5.7 0.2 - + - -
80A VAL* 4.9 8.1 - - + -
82A ILE* 4.1 10.1 - - + -
117A LEU* 4.0 13.9 - - + -
130A TYR* 3.4 5.1 - - - -
131A ILE* 2.7 64.7 + - + +
133A VAL* 3.8 17.9 - - + -
151A VAL* 1.3 75.0 - - - +
153A SER* 1.3 69.7 + - - +
154A ILE* 3.9 23.6 - - + -
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ASP* 3.0 29.7 + - - +
70A GLY 2.9 23.4 + - - -
128A VAL* 3.6 23.5 - - - +
129A HIS 3.1 11.7 - - - -
130A TYR* 4.0 18.4 + - - -
152A PHE* 1.3 77.6 - - - +
154A ILE* 1.3 66.3 + - - +
155A GLU 4.2 0.4 + - - -
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY* 3.3 14.4 - - - +
71A THR 4.2 0.4 - - - -
72A ALA* 4.1 10.8 - - + -
78A PHE* 3.7 41.7 - - + -
107A TRP* 3.8 23.6 - - + -
108A LEU* 4.0 18.2 - - + -
117A LEU* 4.1 3.6 - - + -
127A GLY 3.6 1.9 - - - +
128A VAL* 4.5 0.9 - - - -
129A HIS* 2.9 36.0 + - + +
131A ILE* 3.9 22.4 - - + -
152A PHE* 3.9 17.3 - - + -
153A SER* 1.3 79.8 - - - +
155A GLU* 1.3 62.6 + - - +
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Residues in contact with GLU 155 (chain A).
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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70A GLY 3.1 10.9 + - - +
71A THR* 3.3 5.3 - - + -
72A ALA 2.9 24.9 + - - +
127A GLY* 3.4 9.0 - - - +
128A VAL* 3.9 26.7 - - + +
153A SER* 4.2 0.8 + - - -
154A ILE* 1.3 71.3 - - - +
156A VAL* 1.3 66.5 + - - +
157A TYR* 3.4 45.2 + - + +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA* 3.4 7.4 - - + +
74A VAL* 3.8 21.8 - - + +
107A TRP* 3.4 39.7 - - + -
121A PRO* 3.7 26.0 - - + -
125A ASP 3.3 26.5 - - - +
126A LYS* 3.4 6.9 - - - +
127A GLY* 2.8 27.7 + - - +
129A HIS* 3.8 7.2 - - + -
154A ILE 4.6 0.4 - - - +
155A GLU* 1.3 76.0 - - - +
157A TYR* 1.4 61.7 + - - +
158A PRO* 4.7 0.5 - - - +
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 3.9 30.8 - - + +
72A ALA 2.8 19.3 + - - +
73A VAL* 3.5 5.6 - - + -
74A VAL* 3.0 25.0 + - - +
126A LYS* 4.5 0.7 - - - -
155A GLU* 3.4 43.0 + - + +
156A VAL* 1.4 72.6 - - - +
158A PRO* 1.3 76.2 - - + +
161A HIS* 3.5 46.0 - + + -
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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