Contacts of the strand formed by residues 62 - 70 (chain F) in PDB entry 3SKU
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 ILE 62 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F PHE* 4.9 19.7 - - + -
61F LYS* 1.3 85.5 - - - +
63F THR* 1.3 68.2 + - - +
64F GLN 3.7 17.3 - - - +
65F VAL* 4.8 1.1 - - + -
104F PHE* 3.0 64.4 - - + +
126F PHE* 4.4 12.8 - - + -
127F ALA 3.2 12.1 - - - +
128F THR* 3.3 20.0 - - + -
129F PHE* 4.5 2.4 - - - -
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Residues in contact with THR 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG 5.7 1.4 - - - -
223B PHE* 2.9 53.4 + - + -
62F ILE* 1.3 81.4 - - - +
64F GLN* 1.4 53.9 + - - +
81F TYR 4.9 0.2 - - - -
82F ASN* 2.5 36.0 + - - +
83F PRO* 4.1 4.5 - - - +
104F PHE* 4.6 3.8 - - - -
127F ALA* 2.6 23.8 + - + +
129F PHE* 3.5 23.1 - - + +
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Residues in contact with GLN 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 5.1 0.3 + - - -
220B LEU* 4.9 0.8 - - - +
221B PRO* 2.2 46.8 + - - +
222B ARG* 4.7 9.8 - - - +
62F ILE* 3.7 2.1 - - - +
63F THR* 1.4 81.7 - - - +
65F VAL* 1.3 82.3 + - - +
66F THR* 3.9 16.8 + - - +
80F ILE* 2.9 30.8 - - + +
81F TYR 3.3 6.7 - - - +
82F ASN* 3.2 21.3 + - + +
125F GLU 4.8 0.2 - - - -
126F PHE* 3.8 2.6 - - - -
127F ALA* 2.8 43.4 + - + +
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Residues in contact with VAL 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ILE* 4.8 4.0 - - + -
64F GLN* 1.3 80.8 - - - +
66F THR* 1.3 63.7 + - - +
67F TRP* 5.8 0.2 - - + -
79F ALA 3.8 1.6 - - - +
80F ILE* 3.4 3.6 + - - -
81F TYR* 2.8 62.8 + - + +
99F PHE* 4.3 4.4 - - + -
104F PHE* 4.7 5.4 - - + +
106F ASP 5.4 1.1 - - - +
107F GLY* 3.7 25.8 - - - +
124F CYS* 4.5 11.0 - - - -
125F GLU 3.8 3.4 - - - +
126F PHE* 3.1 39.9 - - + -
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Residues in contact with THR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 3.7 36.1 - - + +
222B ARG* 4.9 1.4 + - - -
64F GLN* 3.9 15.2 + - - +
65F VAL* 1.3 78.2 + - - +
67F TRP* 1.3 66.5 + - - +
68F GLN* 3.5 30.7 - - + +
79F ALA 3.3 5.8 - - - +
80F ILE* 4.1 5.3 - - + +
123F ILE 3.2 4.5 - - - +
124F CYS* 3.3 3.3 - - - -
125F GLU* 2.9 43.7 + - + -
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Residues in contact with TRP 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F VAL* 4.5 7.0 - - + -
49F LEU* 4.1 27.1 - - + -
50F HIS 3.6 24.7 - - - -
51F CYS* 3.9 4.3 - - + -
65F VAL* 5.8 0.2 - - + -
66F THR* 1.3 74.4 - - - +
68F GLN* 1.3 62.9 + - - +
77F ASN* 4.8 0.9 - - - +
78F VAL* 3.0 32.5 + - + -
79F ALA* 2.7 26.4 + - + +
99F PHE* 3.7 23.1 - + - -
107F GLY* 2.4 33.5 + - - -
109F ILE* 3.7 27.6 - - + +
122F TYR* 4.1 29.8 - + + -
123F ILE 3.6 4.0 - - - -
124F CYS* 3.8 31.8 - - + -
138F LEU* 4.6 5.6 - - + -
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Residues in contact with GLN 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLY* 3.4 25.5 + - - -
220B LEU* 3.7 17.8 - - - +
66F THR* 3.5 22.9 - - + +
67F TRP* 1.3 72.7 - - - +
69F LYS* 1.3 61.6 + - - +
75F LYS* 4.8 22.2 + - + +
76F GLN 3.7 5.1 + - - +
77F ASN* 3.0 26.6 + - - +
78F VAL* 4.0 4.0 - - - -
122F TYR* 3.4 6.8 - - - -
123F ILE* 2.6 60.3 + - + +
125F GLU* 5.0 5.4 - - - +
135F GLU* 5.1 2.1 - - - +
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Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLN* 1.3 75.3 - - - +
70F SER* 1.3 61.2 + - - +
71F THR* 3.6 15.6 + - - +
75F LYS* 3.6 2.2 - - - -
76F GLN* 2.7 69.0 + - + +
78F VAL* 4.2 2.9 - - + +
93F TYR* 2.9 27.1 + - - +
117F GLU* 2.6 31.1 + - - +
118F ASP* 3.6 4.8 + - - +
119F GLU 3.7 16.8 - - - -
120F GLY* 5.3 1.3 - - - -
121F VAL 4.0 5.8 - - - +
122F TYR* 3.4 31.5 + - + +
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Residues in contact with SER 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLN 4.1 1.4 + - - -
69F LYS* 1.3 70.9 - - - +
71F THR* 1.3 59.8 + - - +
72F ASN* 2.8 17.2 + - - -
73F GLY 4.2 3.1 + - - -
74F SER 3.4 17.0 + - - -
75F LYS* 4.4 11.9 - - - +
120F GLY* 5.4 0.2 - - - -
121F VAL* 3.4 34.9 + - - +
123F ILE* 3.7 25.2 - - - +
137F GLN* 5.3 0.9 - - - -
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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