Contacts of the strand formed by residues 61 - 71 (chain I) in PDB entry 3STJ
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 61 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31I VAL* 3.7 24.7 - - + -
32I GLU* 3.4 6.8 - - - +
33I GLY* 3.2 34.2 + - - -
34I THR 3.3 42.6 - - - -
59I GLN 4.6 1.6 - - - +
60I PRO* 1.3 75.1 - - - +
62I GLU* 1.3 68.1 + - - +
63I GLY* 3.9 12.3 - - - -
86I GLN* 3.7 47.1 - - + -
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Residues in contact with GLU 62 (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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30I ARG* 3.1 33.6 + - + +
31I VAL 3.3 3.6 - - - +
32I GLU* 3.1 36.8 - - + +
61I PHE* 1.3 78.0 - - - +
63I GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 63 (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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29I VAL 3.9 0.4 - - - +
30I ARG* 3.6 6.9 - - - +
31I VAL* 2.8 40.2 + - - +
61I PHE* 3.9 13.5 - - - -
62I GLU* 1.3 74.9 - - - +
64I LEU* 1.4 59.7 + - - +
83I VAL* 5.9 2.9 - - - -
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Residues in contact with LEU 64 (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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28I SER* 4.8 6.1 - - - -
29I VAL 3.5 9.6 - - - +
30I ARG* 4.8 16.6 - - + +
63I GLY* 1.4 71.1 - - - +
65I GLY* 1.3 76.4 + - - +
83I VAL* 5.0 3.6 - - - -
146I ASN* 3.5 36.1 - - + +
149I GLY* 3.8 23.1 - - - +
185I GLY* 3.6 16.0 + - - -
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Residues in contact with GLY 65 (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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28I SER* 3.8 2.6 - - - -
29I VAL* 2.9 28.3 + - - +
64I LEU* 1.3 84.7 - - - +
66I SER* 1.3 60.6 + - - -
83I VAL* 4.1 15.9 - - - +
146I ASN* 3.9 0.7 - - - +
185I GLY* 3.3 17.5 - - - -
187I SER* 3.7 8.1 - - - -
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Residues in contact with SER 66 (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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26I VAL* 5.1 0.9 - - - -
27I VAL 3.3 11.9 - - - -
29I VAL* 3.5 10.1 - - - +
65I GLY* 1.3 71.6 - - - -
67I GLY* 1.3 60.3 + - - +
79I THR* 3.0 22.2 + - - -
145I GLY* 3.2 8.2 - - - -
146I ASN* 2.9 23.2 + - - +
185I GLY 2.9 17.1 + - - -
186I ASN 4.0 0.8 + - - -
187I SER 2.9 5.9 + - - -
188I GLY* 3.4 8.4 - - - -
189I GLY* 3.5 24.9 - - - -
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Residues in contact with GLY 67 (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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26I VAL* 3.5 11.1 - - - +
27I VAL* 2.8 42.9 + - - -
29I VAL* 3.8 2.6 - - - +
66I SER* 1.3 75.8 - - - +
68I VAL* 1.3 62.8 + - - -
77I VAL* 3.9 5.6 - - - -
78I LEU 3.3 12.6 - - - -
79I THR* 4.4 0.4 - - - -
188I GLY 3.5 3.6 - - - -
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Residues in contact with VAL 68 (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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25I ALA 3.6 5.8 - - - +
26I VAL* 4.8 1.8 - - + -
67I GLY* 1.3 78.4 - - - +
69I ILE* 1.4 64.9 + - - +
70I ILE* 3.2 3.4 + - + +
77I VAL* 3.3 4.8 - - - +
78I LEU* 2.8 39.4 + - + +
127I ILE* 3.7 42.4 - - + -
188I GLY 3.8 4.7 - - - +
189I GLY 3.8 6.7 - - - +
190I ALA* 3.7 35.2 - - + +
198I LEU* 4.1 9.6 - - + -
201I ILE* 4.0 14.4 - - + -
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Residues in contact with ILE 69 (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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24I PRO 4.1 11.4 - - - +
25I ALA 2.8 14.9 + - - +
27I VAL* 3.6 27.8 - - + -
68I VAL* 1.4 68.6 - - - +
70I ILE* 1.3 59.8 + - - +
71I ASN 3.8 26.2 - - - +
72I ALA* 3.8 8.1 - - - +
76I TYR 3.5 7.4 - - - +
77I VAL* 3.9 15.7 - - + -
94I LEU* 4.3 7.4 - - + -
118I ILE* 4.5 3.4 - - + -
124I LEU* 3.9 26.2 - - + -
125I THR 3.3 25.8 - - - +
126I GLN* 3.4 1.4 - - - -
127I ILE* 2.9 32.9 + - - +
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Residues in contact with ILE 70 (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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68I VAL* 3.2 6.9 + - + +
69I ILE* 1.3 73.2 - - - +
71I ASN* 1.4 62.2 + - + +
76I TYR* 2.8 30.8 + - + +
78I LEU* 3.6 33.9 - - + +
115I LEU* 4.3 11.4 - - + -
126I GLN* 3.8 17.6 + - - +
127I ILE* 4.5 12.7 - - + +
129I ILE* 3.8 33.6 - - + +
198I LEU* 5.2 2.5 - - + -
225I ARG* 4.8 6.5 - - + -
228I ALA* 4.1 15.3 - - + -
232I ILE* 6.0 1.6 - - + -
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Residues in contact with ASN 71 (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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69I ILE* 3.8 3.8 - - - +
70I ILE* 1.4 79.0 - - + +
72I ALA* 1.3 52.2 + - - +
73I SER* 3.1 13.7 + - - -
74I LYS* 2.9 40.3 + - - +
75I GLY* 2.8 31.4 + - - -
76I TYR* 3.0 36.7 + - + -
126I GLN* 3.4 7.6 + - - +
232I ILE* 5.9 2.0 - - - +
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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
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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