Contacts of the strand formed by residues 73 - 88 (chain A) in PDB entry 1LKF
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 PHE 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.1 22.9 - - - +
71A TYR 4.4 0.2 + - - -
72A ASP* 1.3 81.6 - - + +
74A SER* 1.3 69.2 + - - +
75A LYS* 4.7 16.2 - - + -
203A ALA* 3.5 2.6 - - - +
253A GLN* 3.3 50.3 - - + -
254A ILE 3.4 10.5 - - - -
255A ARG* 3.5 38.4 - - + +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO* 3.6 6.8 - - - +
70A ASP* 2.9 18.3 + - - -
73A PHE* 1.3 82.1 - - - +
75A LYS* 1.3 69.1 + - - +
203A ALA* 3.5 28.2 - - - +
204A GLY* 3.3 13.4 - - - -
207A PHE* 3.5 14.9 - - - -
253A GLN* 3.2 5.2 - - - +
254A ILE* 2.9 33.3 + - - -
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Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS 4.5 0.9 - - - +
66A PRO* 3.4 20.6 - - - +
67A ASN 4.7 0.5 + - - -
70A ASP* 4.3 4.3 + - - +
73A PHE* 4.7 15.9 - - + -
74A SER* 1.3 79.2 + - - +
76A LEU* 1.3 61.9 + - - +
77A TYR* 3.6 27.6 + - + -
207A PHE* 4.0 5.8 - - - -
251A LEU* 3.5 27.4 - - + +
252A TYR 3.2 11.4 - - - +
253A GLN* 3.7 11.2 - - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 3.9 24.7 - - + -
64A VAL* 3.5 13.0 - - - +
66A PRO* 4.2 14.6 - - + -
75A LYS* 1.3 76.4 - - - +
77A TYR* 1.3 68.0 + - - +
78A TRP* 3.7 19.7 - - + -
193A PHE* 4.2 9.9 - - + -
207A PHE* 3.7 33.2 - - + -
213A MET* 4.5 10.5 - - + -
251A LEU* 3.5 5.9 - - - +
252A TYR* 2.8 53.1 + - + +
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY 4.2 8.7 - - - +
63A PHE* 3.1 14.1 - - - -
64A VAL* 3.0 52.8 + - + +
75A LYS* 3.6 26.7 + - + -
76A LEU* 1.3 78.1 - - - +
78A TRP* 1.3 61.6 + - - +
249A MET* 4.4 15.5 - - + -
250A ASP 3.3 15.7 - - - -
251A LEU* 3.5 37.0 - - + +
269A PHE* 4.2 10.6 - + + -
270A LYS* 3.6 50.3 + - + -
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Residues in contact with TRP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER 4.2 3.8 - - - -
63A PHE* 4.3 7.6 - - + +
76A LEU* 3.7 21.5 - - + -
77A TYR* 1.3 76.0 - - - +
79A GLY* 1.3 65.4 + - - +
80A ALA* 3.2 14.1 + - + -
149A TYR* 3.6 10.5 - - - -
168A ALA* 3.5 34.1 - - + -
171A ILE* 4.1 10.8 - - + -
181A ARG* 3.9 5.8 - - + -
192A LEU* 3.1 27.1 - - + -
193A PHE* 3.5 16.3 - + + -
213A MET* 4.3 3.4 - - + -
217A SER* 3.5 30.1 - - - +
249A MET* 3.2 5.3 - - - -
250A ASP* 2.9 60.6 + - + +
252A TYR* 3.7 6.9 - - + +
265A ASN* 2.9 23.7 + - - -
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER* 3.3 29.5 + - - -
78A TRP* 1.3 69.4 - - - +
80A ALA* 1.3 55.4 + - - -
81A LYS 3.7 1.6 - - - -
82A TYR* 4.2 7.4 - - - -
149A TYR* 2.5 30.4 + - - -
216A LEU 3.4 10.0 - - - +
217A SER* 2.9 16.2 + - - -
247A ARG* 5.6 1.3 - - - -
248A GLU 3.9 5.6 - - - -
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TRP* 3.2 22.1 + - + -
79A GLY* 1.3 74.0 - - - -
81A LYS* 1.3 62.3 + - - +
149A TYR* 3.9 3.8 - - - -
167A GLU* 3.5 2.4 - - - +
168A ALA* 2.8 29.6 + - - +
181A ARG* 3.4 10.5 - - - +
248A GLU 3.0 6.9 + - - +
250A ASP* 3.3 42.4 - - + +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY 3.7 1.0 - - - -
80A ALA* 1.3 79.8 - - - +
82A TYR* 1.3 67.0 + - - +
83A ASN* 3.1 27.0 + - - +
149A TYR* 4.6 0.2 - - - -
152A THR* 5.0 6.7 + - - -
165A GLY* 3.9 14.1 - - - -
166A VAL 3.2 7.0 - - - +
167A GLU* 3.5 39.0 + - + +
181A ARG* 3.6 11.7 - - - +
247A ARG* 3.3 5.2 - - - +
248A GLU* 2.8 59.5 + - + +
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.4 42.4 - - + -
60A ASN 3.6 11.2 - - - -
61A SER* 3.2 20.7 + - - -
79A GLY* 4.2 11.7 - - - -
81A LYS* 1.3 76.1 - - - +
83A ASN* 1.3 62.3 + - - +
84A VAL* 4.2 1.1 + - - -
149A TYR* 4.3 1.6 - + - -
164A TRP 3.7 0.7 - - - +
165A GLY* 3.2 4.0 - - - -
166A VAL* 2.8 48.7 + - + +
216A LEU* 2.5 48.3 + - + -
220A ASN 3.7 5.5 - - - -
221A PHE* 3.6 44.2 - + + -
246A GLN 3.3 5.8 - - - +
247A ARG* 4.2 7.9 - - + -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.1 26.1 + - - +
82A TYR* 1.3 74.0 - - - +
84A VAL* 1.3 64.0 + - - +
85A SER* 4.2 7.4 - - - +
164A TRP 3.3 4.7 - - - +
165A GLY* 3.4 9.7 - - - -
244A THR* 3.5 1.5 - - - +
245A TYR* 3.4 2.6 - - - -
246A GLN* 2.7 69.1 + - + +
248A GLU* 3.0 30.3 + - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 4.8 3.6 - - + -
59A ILE* 3.9 16.2 - - + -
82A TYR 5.5 0.7 - - - -
83A ASN* 1.3 78.7 - - - +
85A SER* 1.3 67.9 + - - +
86A ILE* 4.8 7.6 - - + -
163A GLY* 3.2 2.6 - - - -
164A TRP* 3.0 45.0 + - + +
221A PHE* 5.1 2.2 - - + -
223A PRO* 4.2 4.9 - - + -
225A PHE* 3.9 37.2 - - + -
244A THR 3.1 3.4 - - - -
245A TYR* 3.6 35.0 - - + -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN* 5.0 6.4 - - - +
84A VAL* 1.3 76.8 + - - +
86A ILE* 1.3 66.0 + - - +
87A SER* 6.2 0.9 - - - -
154A SER* 5.5 2.8 + - - -
156A ASN* 5.7 2.6 + - - -
162A VAL 3.5 7.4 - - - -
163A GLY* 4.1 5.5 - - - -
164A TRP 5.3 0.3 + - - -
242A THR 3.7 0.9 - - - +
243A VAL* 3.3 5.9 - - - +
244A THR* 2.8 51.4 + - - +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.9 12.3 - - + +
55A ALA* 4.5 14.6 - - + -
84A VAL* 4.8 2.9 - - + -
85A SER* 1.3 75.6 - - - +
87A SER* 1.3 64.5 + - - +
96A VAL* 5.0 3.8 - - + +
160A LYS 4.2 0.2 - - - +
161A ASN* 3.4 4.0 + - - +
162A VAL* 2.8 44.3 + - + +
164A TRP* 3.9 24.7 - - + -
225A PHE 6.5 0.2 - - - -
227A SER* 3.9 18.6 - - - +
229A LEU* 4.8 5.2 - - + -
241A ILE* 3.8 29.8 - - + -
242A THR 3.4 4.3 - - - +
243A VAL* 4.0 27.4 - - + -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER* 5.7 1.3 - - - -
86A ILE* 1.3 75.5 - - - +
88A SER* 1.3 63.2 + - - +
89A GLN* 3.3 20.7 + - - +
96A VAL* 5.5 0.2 - - - -
160A LYS 3.5 3.7 + - - -
161A ASN* 2.5 28.1 + - - -
241A ILE* 3.2 10.7 - - - -
242A THR* 2.9 48.3 + - - -
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A SER* 1.3 72.8 + - - +
89A GLN* 1.3 61.7 + - - +
90A SER 3.5 7.0 + - - -
94A VAL* 3.5 34.6 + - - +
96A VAL* 4.5 4.1 - - - +
160A LYS* 2.7 49.9 + - - +
161A ASN* 5.3 0.3 - - - +
229A LEU* 4.0 12.5 - - - +
239A SER* 5.0 1.0 + - - -
240A LYS 3.6 8.6 + - - -
241A ILE* 4.6 4.0 - - - +
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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
------------------------------------------------------------
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