Contacts of the strand formed by residues 91 - 99 (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 LEU 91 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84G PHE* 3.6 34.3 - - + -
86G ASN* 3.9 19.3 - - + +
89G GLN 3.7 1.2 + - - -
90G THR* 1.3 74.2 - - - +
92G VAL* 1.3 65.8 + - - +
93G VAL* 4.3 9.6 - - + +
112G LEU* 4.1 9.6 - - + -
130G ILE* 3.9 17.5 - - + -
174G LEU* 3.7 1.4 - - + +
175G ILE* 3.5 2.4 - - - -
176G VAL* 2.8 48.5 + - + +
311G PHE* 3.9 29.2 - - + -
332G ILE* 3.8 16.8 - - + -
333G THR 3.8 3.8 - - - +
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Residues in contact with VAL 92 (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 17.5 - - + -
91G LEU* 1.3 78.5 - - - +
93G VAL* 1.3 66.0 + - - +
94G GLN* 4.7 2.2 - - + -
173G THR* 3.8 17.5 - - + -
174G LEU 3.3 9.4 - - - +
175G ILE* 4.2 9.4 - - + -
331G LEU 3.7 1.1 - - - +
332G ILE* 3.3 9.9 - - - +
333G THR* 2.8 51.1 + - + +
335G ASP 4.1 4.7 - - - +
336G GLU* 4.0 23.8 - - - +
339G ALA* 3.6 24.0 - - + -
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Residues in contact with VAL 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 4.3 13.5 - - + -
92G VAL* 1.3 76.1 - - - +
94G GLN* 1.3 65.4 + - - +
95G PHE* 4.7 3.4 - - + -
110G VAL* 4.1 25.6 - - + -
112G LEU* 3.4 36.8 - - + -
130G ILE* 5.8 1.8 - - + -
132G PHE* 4.0 11.3 - - + -
172G TYR 3.8 0.5 - - - +
173G THR* 3.4 2.3 - - - +
174G LEU* 2.8 55.3 + - + +
314G LEU* 5.0 2.9 - - + -
331G LEU 3.6 4.5 - - - +
332G ILE* 4.8 7.4 - - + +
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Residues in contact with GLN 94 (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* 4.7 4.5 - - + -
93G VAL* 1.3 77.8 - - - +
95G PHE* 1.3 69.1 + - - +
171G LEU* 3.6 21.4 - - + +
172G TYR 3.2 12.3 - - - +
173G THR* 2.8 29.6 + - + +
188G ASN* 4.5 2.6 - - - +
329G ASN 4.2 2.2 + - - +
330G PHE* 3.4 1.2 - - - +
331G LEU* 2.7 46.7 + - + +
339G ALA* 2.9 36.8 + - - +
342G PHE* 4.1 15.4 - - - -
343G GLY* 3.6 17.4 - - - +
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Residues in contact with PHE 95 (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* 4.7 2.7 - - + -
94G GLN* 1.3 84.8 - - - +
96G THR* 1.3 65.8 + - - +
97G VAL* 3.3 31.9 - - + -
108G GLY 3.4 15.0 - - - -
110G VAL* 3.7 39.5 - - + -
132G PHE* 3.6 36.3 - + - -
133G GLY* 4.2 7.4 - - - -
134G PRO* 4.4 0.4 - - + -
171G LEU* 3.7 4.4 - - - +
172G TYR* 2.9 36.6 + - + +
327G PHE* 4.5 7.2 - + - -
328G ASP 3.8 4.9 - - - +
329G ASN 3.5 9.9 - - - -
330G PHE* 3.6 22.2 - + + -
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Residues in contact with THR 96 (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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95G PHE* 1.3 77.2 - - - +
97G VAL* 1.3 64.3 + - - +
169G THR* 3.7 22.2 - - + +
170G HIS 3.3 6.5 - - - +
171G LEU* 3.8 22.9 - - + -
326G ILE 4.4 1.2 + - - -
327G PHE* 3.4 6.6 - - - -
328G ASP* 2.9 55.9 + - - +
329G ASN* 3.5 18.6 + - + +
347G TRP* 4.0 20.0 - - + +
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Residues in contact with VAL 97 (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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95G PHE* 3.3 34.5 - - + -
96G THR* 1.3 75.7 - - - +
98G LYS* 1.3 60.9 + - - +
99G HIS* 3.8 29.3 + - + +
108G GLY* 3.6 9.2 - - - +
134G PRO* 4.2 6.3 - - + -
168G PHE 3.7 2.3 - - - +
169G THR* 3.6 1.5 - - - -
170G HIS* 2.8 37.8 + - - +
172G TYR* 4.1 19.7 - - + -
325G THR* 3.8 17.0 - - + -
326G ILE 3.6 4.3 - - - -
327G PHE* 4.1 9.2 - - + -
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Residues in contact with LYS 98 (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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53G SER 4.6 1.3 - - - -
56G PHE* 2.8 43.0 + - - -
57G TYR* 4.4 1.4 - - - +
97G VAL* 1.3 77.0 - - - +
99G HIS* 1.3 59.8 + - - +
100G GLU* 3.1 40.6 + - + +
167G GLU 3.6 14.6 - - - +
168G PHE 3.7 5.6 - - - +
169G THR* 3.3 24.9 - - + +
324G GLY 4.0 0.9 - - - +
325G THR* 3.3 2.3 - - - -
326G ILE* 2.9 53.9 + - + +
354G GLU* 2.9 18.9 + - - +
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Residues in contact with HIS 99 (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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97G VAL* 3.8 17.5 + - + +
98G LYS* 1.3 71.1 - - - +
100G GLU* 1.3 63.6 + - - +
101G GLN* 3.0 13.5 + - - +
102G ASN* 3.1 8.5 + - - -
103G ILE* 3.7 38.8 - - + +
106G GLY 4.8 1.8 + - - -
107G GLY 4.3 12.3 - - - -
108G GLY* 4.4 4.2 + - - -
134G PRO* 4.7 11.0 - - + +
136G ILE* 4.0 20.0 - - + +
164G LYS 4.6 7.6 - - - -
165G ASP* 5.2 1.6 - - - +
166G ASP 3.6 12.3 + - - +
167G GLU* 3.4 15.7 - - - -
168G PHE 4.3 4.4 + - - -
325G THR* 2.7 38.0 + - + +
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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