Contacts of the strand formed by residues 61 - 71 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31J VAL* 3.7 24.5 - - + -
32J GLU* 3.4 7.3 - - - +
33J GLY* 3.2 33.5 + - - -
34J THR 3.3 42.6 - - - -
59J GLN* 4.6 1.8 - - - +
60J PRO* 1.3 75.1 - - - +
62J GLU* 1.3 65.5 - - - +
63J GLY* 3.9 11.9 - - - -
83J VAL 5.8 0.2 - - - -
86J GLN* 3.7 47.8 - - + -
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Residues in contact with GLU 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ARG* 3.1 34.1 + - + +
31J VAL 3.3 4.0 - - - +
32J GLU* 3.1 37.2 - - + +
61J PHE* 1.3 76.5 - - - +
63J GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J VAL 4.6 0.2 - - - -
30J ARG* 3.6 6.4 - - - +
31J VAL* 2.9 41.8 + - - +
61J PHE* 3.9 12.7 - - - -
62J GLU* 1.3 73.6 - - - +
64J LEU* 1.3 62.4 + - - +
83J VAL* 5.8 3.1 - - - -
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Residues in contact with LEU 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J SER* 3.7 11.7 - - - +
29J VAL 3.5 7.4 - - - +
30J ARG* 4.4 22.0 - - + +
62J GLU 4.5 0.2 + - - -
63J GLY* 1.3 72.2 - - - +
65J GLY* 1.3 76.8 + - - +
83J VAL* 5.0 3.6 - - - -
146J ASN* 3.7 30.5 - - + +
149J GLY* 4.2 19.7 - - - +
185J GLY* 3.8 14.8 + - - -
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Residues in contact with GLY 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J SER* 3.6 5.5 - - - -
29J VAL* 2.8 30.3 + - - +
64J LEU* 1.3 82.4 - - - +
66J SER* 1.3 65.5 + - - -
83J VAL* 4.2 13.9 - - - +
146J ASN* 3.9 1.3 - - - +
185J GLY 3.5 13.5 - - - -
187J SER* 3.9 6.5 - - - -
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Residues in contact with SER 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J VAL* 4.9 0.7 - - - -
27J VAL 3.4 13.5 - - - -
29J VAL* 3.5 9.3 - - - +
65J GLY* 1.3 72.5 - - - -
67J GLY* 1.3 58.7 + - - +
79J THR* 3.0 22.2 + - - -
83J VAL* 4.7 0.2 - - - +
144J VAL 4.8 0.2 - - - -
145J GLY* 3.2 6.6 - - - -
146J ASN* 2.8 32.7 + - - +
185J GLY 3.0 6.6 + - - -
186J ASN 3.7 1.5 + - - -
187J SER 2.8 13.2 + - - +
188J GLY* 3.4 5.8 - - - -
189J GLY* 3.5 24.2 - - - -
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Residues in contact with GLY 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J VAL* 3.3 11.1 - - - +
27J VAL* 3.0 40.8 + - - -
29J VAL* 3.7 6.2 - - - +
66J SER* 1.3 76.0 - - - +
68J VAL* 1.3 62.4 + - - -
77J VAL* 4.0 2.0 - - - -
78J LEU 3.2 13.9 - - - -
79J THR* 4.4 0.2 - - - -
188J GLY 3.3 3.7 + - - -
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Residues in contact with VAL 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ALA 3.8 6.7 - - - +
26J VAL* 4.7 1.8 - - + -
67J GLY* 1.3 77.8 - - - +
69J ILE* 1.4 63.9 + - - +
70J ILE* 3.3 4.3 + - + +
77J VAL* 3.3 5.0 - - - +
78J LEU* 2.8 41.0 + - + +
127J ILE* 3.7 42.6 - - + -
188J GLY 3.8 1.3 - - - +
190J ALA* 3.6 32.8 - - + +
198J LEU* 4.1 8.7 - - + -
201J ILE* 3.6 28.0 - - + -
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Residues in contact with ILE 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J PRO 4.0 8.7 - - - +
25J ALA* 3.0 17.6 + - - +
27J VAL* 3.7 23.1 - - + -
68J VAL* 1.4 68.3 - - - +
70J ILE* 1.3 60.4 + - - +
71J ASN 3.7 26.2 - - - +
72J ALA* 3.8 8.5 - - - +
76J TYR 3.5 6.5 - - - +
77J VAL* 3.9 18.2 - - + -
94J LEU* 4.2 7.4 - - + -
118J ILE* 4.4 3.1 - - + -
124J LEU* 3.9 25.8 - - + -
125J THR 3.3 27.4 - - - +
126J GLN* 4.1 0.9 - - - -
127J ILE* 2.9 32.6 + - - +
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Residues in contact with ILE 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J VAL* 3.3 7.3 + - + +
69J ILE* 1.3 73.6 - - - +
71J ASN* 1.4 61.3 + - + +
76J TYR* 2.7 34.6 + - + +
78J LEU* 3.6 32.3 - - + +
115J LEU* 4.4 10.3 - - + -
126J GLN* 3.9 16.7 - - - +
127J ILE* 4.4 12.3 - - + +
129J ILE* 3.7 34.8 - - + +
198J LEU* 5.3 2.0 - - + -
225J ARG* 4.8 6.1 - - + -
228J ALA* 4.0 18.6 - - + -
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Residues in contact with ASN 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ILE* 3.6 4.6 - - - +
70J ILE* 1.4 79.6 + - + +
72J ALA* 1.3 58.1 + - - +
73J SER* 3.5 10.8 + - - -
74J LYS* 2.8 38.9 + - - +
75J GLY* 3.0 10.0 + - - -
76J TYR* 2.9 55.3 + - + -
126J GLN* 3.4 12.3 + - - +
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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