Contacts of the strand formed by residues 120 - 127 (chain K) in PDB entry 5LS6
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 120 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J CYS* 3.3 13.3 - - - -
98J LEU* 4.0 20.6 - - - +
90K GLU* 4.2 3.0 - - - +
91K ASP* 2.8 38.4 + - - -
92K HIS* 3.6 35.8 - - + +
115K THR 3.9 0.9 - - - +
116K VAL* 3.5 3.1 - - - -
117K GLY 3.0 37.9 + - - +
118K SER* 3.3 1.4 + - - -
119K ASN* 1.3 91.0 + - - +
121K VAL* 1.3 58.1 + - - +
122K THR* 4.1 6.7 + - - +
137K SER* 4.0 14.4 - - - -
138K TYR 2.9 18.8 - - - +
139K VAL* 3.9 13.2 - - + +
147K PHE* 3.5 8.9 - - - -
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Residues in contact with VAL 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J LEU* 4.7 5.4 - - + -
114K ALA* 4.5 2.0 - - + -
115K THR 3.3 4.9 - - - +
116K VAL* 3.7 21.1 - - + -
120K ARG* 1.3 72.9 - - - +
122K THR* 1.3 67.9 + - - +
123K LEU* 4.1 8.7 - - + -
137K SER* 3.3 0.9 + - - -
138K TYR* 2.8 58.4 + - + +
147K PHE* 4.3 2.2 - - + -
163K LEU* 3.4 31.9 - - + -
165K VAL* 4.0 13.7 - - + -
175K ILE* 4.3 12.6 - - + -
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Residues in contact with THR 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J CYS* 4.8 1.8 - - - -
90K GLU* 2.9 23.9 + - - +
114K ALA* 3.3 1.6 - - - -
115K THR* 2.7 50.9 + - - -
120K ARG* 4.1 6.6 - - - +
121K VAL* 1.3 78.3 + - - +
123K LEU* 1.3 63.7 + - - +
124K TYR* 3.4 27.6 - - + +
134K LEU* 3.6 14.6 - - + -
136K GLN 3.4 15.9 - - - +
137K SER* 3.3 14.1 + - - +
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Residues in contact with LEU 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J HIS 6.0 0.4 - - - +
112K VAL* 4.8 8.3 - - + -
113K PHE 3.5 4.0 - - - +
114K ALA* 3.7 19.1 - - + -
121K VAL* 4.1 6.7 - - + -
122K THR* 1.3 77.5 - - - +
124K TYR* 1.3 63.8 + - - +
134K LEU* 3.7 3.8 - - - +
135K LEU* 3.3 31.3 + - + -
136K GLN* 2.9 45.7 + - + +
138K TYR* 4.7 11.2 - - + -
152K TRP* 4.2 21.3 - - + -
163K LEU* 3.8 15.9 - - + -
177K PRO* 3.9 17.5 - - + -
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Residues in contact with TYR 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J VAL* 4.1 19.8 - - + +
88K LEU* 4.3 5.2 - - + -
90K GLU* 3.0 39.0 + - - +
112K VAL* 3.2 7.1 - - - +
113K PHE* 2.7 71.2 + + + +
115K THR* 3.5 26.5 - - + -
122K THR* 3.4 16.6 - - + +
123K LEU* 1.3 73.9 - - - +
125K GLU* 1.3 60.8 + - - +
132K ILE* 3.6 24.0 - - + -
133K ARG 3.4 11.4 - - - +
134K LEU* 3.4 28.5 - - + -
135K LEU* 4.3 1.6 - - - -
434K ILE* 3.6 10.5 - - + +
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Residues in contact with GLU 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J VAL* 3.1 29.7 - - + +
70J ILE* 3.8 9.5 - - - +
110K PRO* 3.1 31.4 - - + +
111K LEU 3.4 7.4 - - - +
112K VAL* 4.2 0.4 - - + +
124K TYR* 1.3 74.9 - - - +
126K CYS* 1.3 64.9 + - - +
127K HIS* 2.9 30.1 + - - +
132K ILE* 3.4 2.9 - - - -
133K ARG* 2.7 39.5 + - + +
135K LEU* 3.4 29.5 - - + +
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Residues in contact with CYS 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K PHE* 3.9 24.2 - - - -
110K PRO* 4.4 3.5 - - - +
111K LEU* 2.8 28.3 + - + +
113K PHE* 4.0 18.2 - - - -
125K GLU* 1.3 74.6 - - - +
127K HIS* 1.3 64.7 + - - +
128K SER 4.3 0.2 - - - -
131K GLU 3.8 4.5 - - - -
132K ILE* 4.4 3.6 - - - +
424K ILE* 3.6 38.6 - - + -
426K ILE* 4.8 0.4 - - - -
436K ARG* 4.0 15.9 - - - +
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Residues in contact with HIS 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K PRO* 4.8 4.2 - - + +
125K GLU* 2.9 45.3 + - - -
126K CYS* 1.3 74.9 + - - +
128K SER* 1.3 69.5 + - - +
131K GLU* 2.9 39.8 + - - +
133K ARG* 3.2 54.8 + - + +
436K ARG* 3.5 6.6 + - - -
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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