Contacts of the strand formed by residues 91 - 99 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D PHE* 3.6 33.7 - - + -
86D ASN* 4.0 19.3 - - + +
89D GLN 3.7 0.6 + - - -
90D THR* 1.3 74.7 - - - +
92D VAL* 1.3 67.6 + - - +
93D VAL* 4.3 9.1 - - + +
112D LEU* 4.3 9.6 - - + -
130D ILE* 3.9 18.2 - - + -
174D LEU 3.7 1.0 - - - +
175D ILE* 3.5 2.3 - - - -
176D VAL* 2.8 50.5 + - + +
311D PHE* 3.8 29.6 - - + -
332D ILE* 3.8 16.8 - - + -
333D THR 3.7 4.0 - - - +
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D THR* 4.0 16.8 - - + -
91D LEU* 1.3 79.6 - - - +
93D VAL* 1.3 66.8 + - - +
94D GLN* 4.7 2.2 - - + -
173D THR* 3.8 17.0 - - + -
174D LEU 3.3 8.7 - - - +
175D ILE* 4.2 10.8 - - + -
331D LEU 3.6 1.0 - - - +
332D ILE* 3.3 9.2 - - - +
333D THR* 2.8 48.8 + - + +
335D ASP 4.0 4.3 - - - +
336D GLU* 4.0 24.0 - - - +
339D ALA* 3.6 25.1 - - + -
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 4.3 14.1 - - + -
92D VAL* 1.3 74.8 - - - +
94D GLN* 1.3 64.6 + - - +
95D PHE* 4.7 3.4 - - + -
110D VAL* 4.1 26.0 - - + -
112D LEU* 3.3 34.1 - - + -
130D ILE* 5.7 1.3 - - + -
132D PHE* 4.0 11.3 - - + -
172D TYR 3.8 0.5 - - - +
173D THR* 3.4 2.1 - - - +
174D LEU* 2.8 57.3 + - + +
314D LEU* 5.0 2.9 - - + -
331D LEU 3.6 4.3 - - - +
332D ILE* 4.7 9.9 - - + +
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D VAL* 4.7 4.9 - - + -
93D VAL* 1.3 79.2 - - - +
95D PHE* 1.3 70.4 + - - +
171D LEU* 3.7 21.0 - - + +
172D TYR 3.2 13.0 - - - +
173D THR* 2.8 30.0 + - + +
188D ASN* 4.6 2.4 - - - +
329D ASN 4.2 1.9 + - - +
330D PHE* 3.4 1.2 - - - +
331D LEU* 2.8 47.3 + - + +
339D ALA* 3.0 36.7 + - - +
342D PHE* 4.1 14.8 - - - -
343D GLY* 3.5 18.2 - - - +
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Residues in contact with PHE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 4.7 2.0 - - + -
94D GLN* 1.3 85.4 - - - +
96D THR* 1.3 65.3 + - - +
97D VAL* 3.2 31.9 - - + -
108D GLY 3.4 14.1 - - - -
110D VAL* 3.6 39.7 - - + -
132D PHE* 3.6 35.9 - + - -
133D GLY* 4.3 4.5 - - - -
171D LEU* 3.7 3.7 - - - +
172D TYR* 2.9 40.8 + - + +
327D PHE* 4.5 7.0 - + - -
328D ASP 3.8 4.9 - - - +
329D ASN 3.5 9.9 - - - -
330D PHE* 3.6 21.8 - + + -
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Residues in contact with THR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PHE* 1.3 76.5 - - - +
97D VAL* 1.3 65.5 + - - +
169D THR* 3.7 22.8 - - + +
170D HIS 3.3 6.3 - - - +
171D LEU* 3.8 23.6 - - + -
326D ILE 4.4 1.2 + - - -
327D PHE* 3.4 6.6 - - - -
328D ASP* 2.9 55.4 + - - +
329D ASN* 3.6 18.2 + - + +
347D TRP* 4.0 19.3 - - + +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PHE* 3.2 34.5 - - + -
96D THR* 1.3 73.1 - - - +
98D LYS* 1.3 61.2 + - - +
99D HIS* 3.8 30.4 + - + +
108D GLY 3.6 9.2 - - - +
134D PRO* 4.2 5.6 - - + -
168D PHE 3.7 2.1 - - - +
169D THR* 3.6 1.1 - - - -
170D HIS* 2.8 37.8 + - - +
172D TYR* 4.1 19.7 - - + -
325D THR* 3.9 16.8 - - + -
326D ILE 3.6 3.6 - - - -
327D PHE* 4.1 9.2 - - + -
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Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D SER 4.6 2.0 + - - -
56D PHE* 2.8 44.4 + - - -
57D TYR* 4.4 1.0 - - - +
97D VAL* 1.3 75.9 - - - +
99D HIS* 1.3 59.2 + - - +
100D GLU* 3.1 40.9 + - + +
167D GLU 3.5 15.9 - - - +
168D PHE 3.7 6.1 - - - +
169D THR* 3.3 24.9 - - + +
324D GLY 4.0 0.3 - - - +
325D THR* 3.3 2.5 - - - -
326D ILE* 2.9 51.6 + - + +
354D GLU* 2.9 18.5 + - - +
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Residues in contact with HIS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL* 3.8 16.4 - - + +
98D LYS* 1.3 70.4 - - - +
100D GLU* 1.3 59.3 + - - +
101D GLN* 3.0 16.6 + - - +
102D ASN* 3.1 9.5 + - - -
103D ILE* 3.7 39.9 - - + +
106D GLY 4.8 2.0 + - - -
107D GLY 4.3 13.0 - - - -
108D GLY* 4.5 3.1 + - - -
134D PRO* 4.7 11.2 + - + +
136D ILE* 4.1 19.8 - - + +
164D LYS 4.6 7.6 - - - -
165D ASP* 5.3 1.6 - - - +
166D ASP 3.6 12.9 + - - +
167D GLU* 3.4 15.9 - - - -
168D PHE 4.3 4.2 + - - -
325D 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