Contacts of the strand formed by residues 169 - 176 (chain G) in PDB entry 5LK5
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 THR 169 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63G ASP* 5.9 0.2 - - - +
96G THR* 3.7 33.2 - - + +
97G VAL 3.6 5.6 - - - +
98G LYS* 3.3 17.4 - - + +
168G PHE* 1.3 72.1 - - - +
170G HIS* 1.3 68.0 + - - +
329G ASN* 5.9 0.9 - - - +
347G TRP* 3.3 26.1 + - + -
350G THR* 4.0 17.9 - - + +
351G LYS* 6.1 0.7 - - - -
354G GLU* 2.5 38.3 + - - +
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Residues in contact with HIS 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G THR* 3.3 5.3 - - - -
97G VAL 2.8 37.9 + - - +
164G LYS* 3.4 36.0 - - + +
166G ASP* 2.7 36.2 + - - -
168G PHE* 3.4 27.3 + - + -
169G THR* 1.3 81.1 + - - +
171G LEU* 1.3 61.7 + - - +
172G TYR* 3.7 22.2 - - + -
186G ILE* 4.7 1.3 - - + -
187G ASP* 2.8 28.6 + - - +
347G TRP* 4.4 2.0 - - - -
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Residues in contact with LEU 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G GLN* 3.6 32.5 - - + +
95G PHE* 3.7 6.5 - - - +
96G THR* 3.8 20.6 - - + -
170G HIS* 1.3 70.5 - - - +
172G TYR* 1.3 60.3 + - - +
173G THR* 4.1 7.2 - - - +
185G LYS 3.7 0.6 - - - +
186G ILE* 3.2 10.6 - - - +
187G ASP* 2.8 38.9 + - - -
188G ASN* 3.8 32.5 - - + +
329G ASN 5.4 2.0 - - - +
343G GLY* 3.7 26.2 - - - -
346G THR* 4.8 3.1 - - - +
347G TRP* 3.9 23.1 - - + -
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Residues in contact with TYR 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL 3.8 0.3 - - - +
94G GLN* 3.2 6.2 - - - +
95G PHE* 2.9 43.2 + - + +
97G VAL* 4.1 15.9 - - + -
132G PHE* 3.9 17.8 - + + -
134G PRO* 3.7 34.5 - - + +
144G VAL* 4.0 22.7 - - + -
163G CYS* 3.5 5.5 - - - +
164G LYS* 3.0 34.7 + - - +
170G HIS* 3.7 27.8 - - + -
171G LEU* 1.3 72.7 - - - +
173G THR* 1.3 62.2 + - - +
184G VAL* 5.8 0.2 - - + -
185G LYS 3.6 1.3 - - - -
186G ILE* 3.7 36.6 - - + -
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Residues in contact with THR 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G VAL* 3.8 23.3 - - + -
93G VAL 3.4 3.1 - - - +
94G GLN* 2.8 29.6 + - - +
132G PHE* 3.5 8.0 - - - -
171G LEU* 4.1 10.0 - - - +
172G TYR* 1.3 74.9 - - - +
174G LEU* 1.3 62.2 + - - +
175G ILE* 4.1 13.5 - - + -
183G GLU 3.9 0.7 - - - +
184G VAL* 3.4 5.0 - - - -
185G LYS* 2.9 60.1 + - + +
188G ASN* 4.7 1.8 + - - +
339G ALA* 4.8 2.7 - - + -
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Residues in contact with LEU 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU 3.7 1.2 - - - +
92G VAL* 3.3 5.7 - - - +
93G VAL* 2.8 47.5 + - + +
130G ILE* 4.1 19.7 - - + -
132G PHE* 3.5 39.0 - - + -
146G VAL* 3.9 25.8 - - + -
148G PHE* 5.2 0.9 - - + -
173G THR* 1.3 73.4 - - - +
175G ILE* 1.3 71.2 - - - +
176G VAL* 4.0 22.2 - - + -
182G TYR* 4.6 6.7 - - + -
183G GLU 3.7 8.7 - - - +
184G VAL* 4.0 12.6 - - + -
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Residues in contact with ILE 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G THR* 4.0 11.7 - - + -
91G LEU 3.5 2.5 - - - +
92G VAL* 4.2 8.1 - - + -
173G THR* 4.1 12.3 - - + -
174G LEU* 1.3 78.0 - - - +
176G VAL* 1.3 63.4 + - - +
177G ARG* 4.0 15.3 - - + +
182G TYR* 3.0 9.2 - - - +
183G GLU* 2.8 53.5 + - + +
185G LYS* 4.3 28.0 - - + +
336G GLU* 3.7 52.7 - - + +
339G ALA* 6.1 0.4 - - + -
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Residues in contact with VAL 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G ASN* 4.7 2.9 + - - +
89G GLN 4.0 1.4 - - - +
90G THR* 3.4 2.3 - - - +
91G LEU* 2.8 56.5 + - + +
130G ILE* 5.1 1.3 - - + -
148G PHE* 3.9 30.1 - - + -
174G LEU* 4.0 22.9 - - + -
175G ILE* 1.3 79.4 - - - +
177G ARG* 1.3 64.6 + - - +
181G THR 3.7 5.6 - - - +
182G TYR* 4.7 2.9 - - + -
196G LEU* 4.8 4.0 - - + -
306G TYR* 3.8 37.2 - - + +
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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
------------------------------------------------------------
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