Contacts of the strand formed by residues 73 - 84 (chain I) 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 ARG 73 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I ASP* 3.4 30.4 + - - +
46I PHE 4.8 0.2 - - - -
47I GLY* 3.8 12.6 - - - +
70I GLN* 3.9 33.9 + - + +
71I LYS 3.1 19.8 + - - +
72I ALA* 1.3 103.8 + - - +
74I PHE* 1.3 59.5 - - - +
75I TYR* 3.4 24.7 - - + -
319I TRP* 3.3 8.0 - - - -
320I GLN 3.0 28.6 + - - -
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Residues in contact with PHE 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LYS* 3.4 33.7 - - - +
45I ASP 5.1 1.6 + - - -
46I PHE* 3.3 15.9 - - + -
47I GLY 2.8 29.6 + - - -
73I ARG* 1.3 74.3 - - - +
75I TYR* 1.3 57.0 + - - +
318I LEU* 3.3 8.3 - - - -
319I TRP* 3.7 44.0 - + + -
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Residues in contact with TYR 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I PHE* 4.4 2.6 - - - -
47I GLY* 3.4 34.8 - - - -
48I LYS 3.6 12.3 - - - -
49I PHE* 3.7 31.4 - + + -
68I THR* 3.5 28.8 - - + -
69I SER 3.5 3.1 + - - -
70I GLN* 2.5 41.6 + - - +
73I ARG* 3.4 27.1 - - + -
74I PHE* 1.3 74.0 - - - +
76I ALA* 1.3 65.8 + - - +
316I LEU 3.7 2.9 - - - +
317I ASP* 3.3 5.9 - - - +
318I LEU* 2.7 48.2 + - + +
320I GLN* 4.1 9.6 - - + -
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I GLU* 3.8 4.2 - - - +
40I SER* 3.0 42.8 + - - +
46I PHE* 3.7 27.6 - - + +
47I GLY 5.2 1.4 + - - -
49I PHE* 4.5 2.2 - - - -
75I TYR* 1.3 77.7 - - - +
77I LEU* 1.3 59.4 + - - +
122I MET* 3.4 17.3 - - + +
316I LEU 3.3 5.8 - - - -
317I ASP* 3.9 6.7 - - - +
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Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PRO* 4.8 2.0 - - + -
33I TRP* 4.1 16.2 - - + -
37I TRP* 3.7 33.4 - - + -
38I ILE 3.5 20.4 - - - +
39I GLU* 3.5 31.6 - - + +
49I PHE* 3.7 34.3 - - + -
66I LEU* 3.8 20.6 - - + -
76I ALA* 1.3 73.6 - - - +
78I SER* 1.3 62.9 + - - +
122I MET* 3.3 2.0 - - - +
316I LEU* 2.8 32.4 + - + +
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Residues in contact with SER 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I TRP* 3.2 8.8 - - - -
38I ILE 2.8 39.5 + - - -
77I LEU* 1.3 72.0 + - - +
79I ALA* 1.3 61.4 + - - +
119I GLN* 3.3 26.1 - - - +
122I MET* 3.0 33.7 - - - +
313I VAL* 3.6 16.9 - - - +
314I LEU 3.4 5.6 - - - -
315I GLY* 3.7 1.7 - - - -
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Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I PHE* 3.6 32.5 - - + -
36I ARG* 3.6 16.8 - - + +
37I TRP* 3.6 20.1 - - + +
78I SER* 1.3 74.9 - - - +
80I SER* 1.3 62.8 + - - +
81I PHE* 3.8 4.0 - - - -
119I GLN* 4.0 2.7 - - - -
313I VAL* 3.3 2.2 - - - -
314I LEU* 2.9 37.0 + - - +
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Residues in contact with SER 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I PHE* 4.3 8.3 - - - -
36I ARG 4.2 5.6 + - - +
79I ALA* 1.3 75.0 - - - +
81I PHE* 1.3 66.3 + - - +
115I ASN* 5.0 5.6 - - - -
119I GLN* 3.5 27.2 + - - -
312I GLY 3.2 12.1 - - - -
313I VAL* 4.1 5.2 - - - -
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Residues in contact with PHE 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I TYR* 3.4 24.2 - - + +
23I PHE* 4.0 22.9 - + + -
79I ALA 3.8 4.3 - - - -
80I SER* 1.3 81.0 - - - +
82I GLU* 1.3 78.3 + - - +
83I PRO* 3.0 10.1 - - - +
84I PHE* 3.7 19.5 - + - -
112I LEU* 4.8 2.2 - - + -
115I ASN* 4.5 2.1 + - - -
311I PHE* 3.4 30.3 - - + -
312I GLY* 2.9 24.4 + - - +
313I VAL 3.6 7.6 - - - -
314I LEU* 3.5 30.3 - - + -
332I ILE* 4.4 15.5 - - + -
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Residues in contact with GLU 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I TYR* 4.8 6.6 + - - +
81I PHE* 1.3 83.4 - - - +
83I PRO* 1.3 89.5 - - - +
84I PHE* 4.2 4.9 - - - +
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Residues in contact with PRO 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I PHE 3.0 6.3 - - - +
82I GLU* 1.3 108.7 - - - +
84I PHE* 1.3 61.2 + - - +
115I ASN* 3.7 32.1 - - + +
310I ASN* 3.9 18.8 - - - +
311I PHE 3.0 16.2 - - - +
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Residues in contact with PHE 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I TYR* 3.5 67.8 - + + -
81I PHE* 3.7 21.3 - + - -
82I GLU 4.2 1.6 - - - +
83I PRO* 1.3 77.5 - - - +
85I SER* 1.3 76.1 + - - +
86I ASN* 4.3 4.7 - - + -
91I LEU* 3.6 25.6 - - + -
112I LEU* 5.8 0.9 - - + -
309I ASP 4.2 2.5 - - - -
310I ASN* 3.4 3.2 - - - -
311I PHE* 2.7 66.3 + + + +
332I ILE* 3.9 7.6 - - + -
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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