Contacts of the strand formed by residues 91 - 99 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H TYR* 5.0 0.4 - - + -
84H PHE* 3.6 33.9 - - + -
86H ASN* 3.9 21.3 - - + +
89H GLN 3.7 0.8 + - - -
90H THR* 1.3 74.6 - - - +
92H VAL* 1.3 66.5 + - - +
93H VAL* 4.3 9.9 - - + -
112H LEU* 4.3 13.9 - - + -
130H ILE* 4.6 8.7 - - + -
174H LEU* 3.7 1.8 - - + +
175H ILE* 3.6 2.3 - - - -
176H VAL* 2.8 54.0 + - + +
311H PHE* 3.9 28.5 - - + -
332H ILE* 3.8 16.2 - - + -
333H THR 3.8 3.6 - - - +
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Residues in contact with VAL 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H THR* 4.0 16.6 - - + -
91H LEU* 1.3 78.7 - - - +
93H VAL* 1.3 67.7 + - - +
94H GLN* 4.7 2.2 - - + -
173H THR* 3.8 17.7 - - + -
174H LEU 3.3 9.4 - - - +
175H ILE* 4.0 15.9 - - + -
331H LEU 3.7 0.5 - - - +
332H ILE* 3.3 9.2 - - - +
333H THR* 2.8 47.7 + - + +
335H ASP 4.1 5.6 - - - +
336H GLU* 4.0 17.9 - - - +
339H ALA* 3.6 23.8 - - + -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H LEU* 4.3 14.1 - - + -
92H VAL* 1.3 75.2 - - - +
94H GLN* 1.3 64.7 + - - +
95H PHE* 4.7 2.9 - - + -
110H VAL* 4.1 26.2 - - + -
112H LEU* 3.3 34.1 - - + -
130H ILE* 5.7 1.6 - - + -
132H PHE* 3.9 11.8 - - + -
172H TYR 3.8 0.7 - - - +
173H THR* 3.4 1.7 - - - +
174H LEU* 2.8 55.3 + - + +
314H LEU* 5.0 3.1 - - + -
331H LEU 3.7 4.7 - - - +
332H ILE* 4.7 10.1 - - + +
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Residues in contact with GLN 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H VAL* 4.7 4.9 - - + -
93H VAL* 1.3 79.2 - - - +
95H PHE* 1.3 70.4 + - - +
171H LEU* 3.7 21.0 - - + +
172H TYR 3.2 13.0 - - - +
173H THR* 2.8 30.0 + - + +
188H ASN* 4.6 1.9 - - - +
329H ASN 4.2 2.0 + - - +
330H PHE* 3.4 1.0 - - - +
331H LEU* 2.8 46.8 + - + +
339H ALA* 2.9 36.7 + - - +
342H PHE* 4.1 14.8 - - - -
343H GLY* 3.6 18.0 - - - +
346H THR* 5.3 0.2 + - - -
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Residues in contact with PHE 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H VAL* 4.7 1.3 - - + -
94H GLN* 1.3 83.8 - - - +
96H THR* 1.3 65.6 + - - +
97H VAL* 3.3 31.6 - - + -
108H GLY 3.4 13.7 - - - -
110H VAL* 3.6 40.6 - - + -
132H PHE* 3.6 37.5 - + - -
133H GLY* 4.2 7.9 - - - -
134H PRO* 4.6 0.9 - - + -
170H HIS 3.9 0.2 - - - +
171H LEU* 3.7 3.9 - - - +
172H TYR* 2.9 37.9 + - + +
314H LEU* 6.1 0.2 - - + -
327H PHE* 4.5 6.7 - + - -
328H ASP 3.8 3.8 - - - +
329H ASN 3.6 9.9 - - - -
330H PHE* 3.6 22.0 - + + -
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Residues in contact with THR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H PHE* 1.3 77.3 - - - +
97H VAL* 1.3 65.2 + - - +
169H THR* 3.6 22.7 - - + +
170H HIS 3.3 6.1 - - - +
171H LEU* 3.8 23.1 - - + -
326H ILE 4.4 0.8 + - - -
327H PHE* 3.4 6.6 - - - -
328H ASP* 2.9 56.6 + - - +
329H ASN* 3.5 18.7 + - + +
347H TRP* 4.0 20.0 - - + +
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Residues in contact with VAL 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H PHE* 3.3 35.4 - - + -
96H THR* 1.3 74.3 - - - +
98H LYS* 1.3 61.6 + - - +
99H HIS* 3.8 29.5 + - + +
108H GLY 3.6 9.2 - - - +
134H PRO* 4.2 7.0 - - + -
168H PHE 3.7 2.1 - - - +
169H THR* 4.4 1.1 - - - -
170H HIS* 2.8 39.4 + - - +
172H TYR* 4.1 19.9 - - + -
325H THR* 3.8 17.5 - - + -
326H ILE 3.6 3.6 - - - -
327H PHE* 4.1 8.1 - - + -
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Residues in contact with LYS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H SER 4.7 1.8 - - - -
56H PHE* 2.8 42.6 + - - -
57H TYR* 4.4 1.2 - - - +
97H VAL* 1.3 76.2 - - - +
99H HIS* 1.3 60.7 + - - +
100H GLU* 3.1 39.0 + - + +
167H GLU 3.6 15.0 - - - +
168H PHE 3.7 6.1 - - - +
169H THR* 3.3 24.5 - - + +
324H GLY 4.0 0.7 - - - +
325H THR* 3.3 2.1 - - - -
326H ILE* 2.9 55.2 + - + +
354H GLU* 2.9 19.1 + - - +
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Residues in contact with HIS 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H VAL* 3.8 17.9 + - + +
98H LYS* 1.3 70.5 - - - +
100H GLU* 1.3 60.5 + - - +
101H GLN* 3.0 15.2 + - - +
102H ASN* 3.1 9.0 + - - -
103H ILE* 3.7 39.8 - - + +
106H GLY 4.8 1.3 + - - -
107H GLY 4.3 13.9 - - - -
108H GLY* 4.4 2.8 + - - -
134H PRO* 4.7 11.1 + - + +
136H ILE* 4.0 20.3 - - + +
164H LYS 4.6 7.9 - - - -
165H ASP* 5.3 1.3 - - - +
166H ASP 3.6 12.7 + - - +
167H GLU* 3.4 15.8 - - - -
168H PHE 4.3 4.9 + - - -
325H THR* 2.7 38.4 + - + +
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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