Contacts of the strand formed by residues 61 - 71 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31H VAL* 3.7 24.0 - - + -
32H GLU* 3.4 6.6 - - - +
33H GLY* 3.2 34.1 + - - +
34H THR 3.3 43.7 - - - -
59H GLN* 4.6 1.6 - - - +
60H PRO* 1.4 75.6 - - - +
62H GLU* 1.3 67.7 + - - +
63H GLY* 3.9 12.1 - - - -
86H GLN* 3.7 47.3 - - + -
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Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ARG* 3.1 33.9 + - + +
31H VAL 3.3 3.6 - - - +
32H GLU* 3.2 35.9 - - + +
61H PHE* 1.3 78.0 - - - +
63H GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ARG* 3.6 6.4 - - - +
31H VAL* 2.8 40.8 + - - +
61H PHE* 3.9 14.1 - - - -
62H GLU* 1.3 74.0 - - - +
64H LEU* 1.3 62.8 + - - +
83H VAL* 5.8 2.5 - - - -
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Residues in contact with LEU 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H SER* 3.4 25.1 - - - +
29H VAL 3.5 8.7 - - - +
30H ARG* 4.4 20.0 - - + +
63H GLY* 1.3 73.2 - - - +
65H GLY* 1.3 70.5 - - - +
83H VAL* 5.0 3.8 - - - -
146H ASN* 3.5 26.2 - - + +
149H GLY* 4.2 20.9 - - - +
185H GLY* 3.9 14.9 + - - -
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Residues in contact with GLY 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H SER* 3.6 5.0 - - - -
29H VAL* 2.8 32.3 + - - -
64H LEU* 1.3 81.9 - - - +
66H SER* 1.3 62.4 + - - -
83H VAL* 4.1 13.2 - - - +
146H ASN* 4.0 0.7 - - - +
185H GLY* 3.6 13.2 - - - -
187H SER* 3.8 9.2 - - - -
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Residues in contact with SER 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H VAL* 4.8 1.6 - - - -
27H VAL 3.1 13.0 + - - -
29H VAL* 3.4 11.1 - - - +
65H GLY* 1.3 74.4 + - - -
67H GLY* 1.3 56.3 + - - +
79H THR* 2.6 29.5 + - - -
145H GLY* 3.3 6.7 - - - -
146H ASN* 2.9 31.4 + - - +
185H GLY 3.2 6.3 + - - -
186H ASN 4.3 0.8 + - - -
187H SER 3.0 7.8 + - - -
188H GLY* 3.7 5.8 - - - -
189H GLY* 3.6 24.2 - - - -
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Residues in contact with GLY 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H VAL* 3.4 9.8 - - - +
27H VAL* 2.8 45.0 + - - -
29H VAL* 4.1 1.1 - - - -
66H SER* 1.3 77.0 - - - +
68H VAL* 1.3 61.7 + - - -
77H VAL* 3.9 5.2 - - - -
78H LEU 3.1 13.0 - - - -
79H THR* 4.3 0.4 - - - -
188H GLY 3.4 4.4 + - - -
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Residues in contact with VAL 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ALA 3.5 6.1 - - - +
26H VAL* 4.8 1.1 - - + -
67H GLY* 1.3 79.1 - - - +
69H ILE* 1.4 63.8 + - - +
70H ILE* 3.3 3.9 + - + +
77H VAL* 3.3 5.2 - - - +
78H LEU* 2.8 43.7 + - + +
127H ILE* 3.6 42.6 - - + -
188H GLY 3.8 4.0 - - - +
189H GLY 3.8 5.8 - - - +
190H ALA* 3.6 36.3 - - + +
198H LEU* 4.1 15.3 - - + -
201H ILE* 4.6 4.0 - - + -
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Residues in contact with ILE 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PRO 4.0 8.3 - - - +
25H ALA* 2.8 17.3 + - - +
27H VAL* 3.6 27.4 - - + -
68H VAL* 1.4 68.1 - - - +
70H ILE* 1.3 59.6 + - - +
71H ASN 3.8 6.3 - - - +
72H ALA* 3.8 28.9 - - - +
76H TYR 3.5 7.0 - - - +
77H VAL* 3.9 14.8 - - + -
94H LEU* 4.2 8.1 - - + -
118H ILE* 4.5 2.9 - - + -
124H LEU* 3.8 24.9 - - + -
125H THR 3.3 27.6 - - - +
126H GLN* 3.4 1.2 - - - -
127H ILE* 2.9 32.7 + - - +
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Residues in contact with ILE 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H VAL* 3.3 6.9 + - + +
69H ILE* 1.3 74.7 - - - +
71H ASN* 1.4 62.4 + - + +
76H TYR* 2.8 31.5 + - + +
78H LEU* 3.6 35.2 - - + +
115H LEU* 4.3 9.9 - - + -
126H GLN* 3.9 15.7 + - - +
127H ILE* 4.3 12.7 - - + +
129H ILE* 3.7 33.5 - - + +
198H LEU* 5.3 1.8 - - + -
225H ARG* 4.8 7.2 - - + +
228H ALA* 4.2 14.4 - - + -
232H ILE* 6.2 1.1 - - + -
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Residues in contact with ASN 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H ILE* 3.8 3.7 - - - +
70H ILE* 1.4 79.2 - - + +
72H ALA* 1.3 52.4 + - - +
73H SER* 3.1 14.2 + - - -
74H LYS* 3.0 40.3 + - - +
75H GLY* 2.8 31.0 + - - -
76H TYR* 3.0 36.6 + - + -
126H GLN* 3.4 7.9 + - - +
232H ILE* 6.2 1.0 - - - +
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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