Contacts of the strand formed by residues 102 - 108 (chain H) in PDB entry 3T30
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 VAL 102 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30H TRP 3.7 1.4 - - - +
31H THR* 3.2 2.8 - - - -
32H PHE* 2.8 36.5 + - + +
44H LEU* 4.3 13.9 - - + -
64H ILE* 4.0 20.4 - - + -
65H LEU 5.6 0.4 - - - -
98H LEU* 3.8 28.3 - - + -
99H SER 3.6 16.8 - - - +
100H PRO* 4.0 5.6 - - + -
101H PRO* 1.3 78.0 - - - +
103H THR* 1.3 64.1 + - - +
104H PHE* 3.7 35.6 - - + -
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Residues in contact with THR 103 (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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29H THR* 4.6 9.9 - - - -
30H TRP 3.4 3.8 - - - +
31H THR* 2.8 29.2 + - - +
33H ARG* 5.1 2.9 + - - -
64H ILE* 3.2 6.1 - - - +
65H LEU* 2.8 70.5 + - + -
66H PRO 5.2 2.7 + - - -
101H PRO* 4.3 0.9 - - - +
102H VAL* 1.3 73.5 - - - +
104H PHE* 1.3 71.9 + - - +
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Residues in contact with PHE 104 (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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19H TRP* 3.6 31.0 - + - -
21H CYS* 4.7 4.7 - - - -
23H LEU* 4.1 21.4 - - + +
28H ARG 3.8 0.6 - - - +
29H THR* 3.2 7.3 - - - -
30H TRP* 2.8 40.2 + + + +
32H PHE* 5.5 0.7 - - + -
44H LEU* 3.9 12.8 - - + -
46H LEU* 4.3 7.0 - - + -
62H VAL* 4.5 2.2 - - + -
63H GLU 3.4 3.6 - - - +
64H ILE* 3.8 23.8 - - + -
80H ILE* 3.7 24.0 - - + -
98H LEU* 3.9 13.0 - - + -
102H VAL* 3.7 24.2 - - + -
103H THR* 1.3 75.7 - - - +
105H GLN* 1.3 61.7 + - - +
115H LEU* 3.6 22.2 - - + -
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Residues in contact with GLN 105 (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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23H LEU* 4.2 5.2 - - - -
28H ARG* 3.3 34.7 - - - +
29H THR* 3.4 22.4 - - + +
62H VAL* 3.4 2.4 - - - -
63H GLU* 2.9 58.6 + - + +
65H LEU* 3.4 28.1 - - + +
103H THR 4.0 0.6 + - - -
104H PHE* 1.3 76.2 - - - +
106H LEU* 1.3 74.3 + - - +
107H ARG* 3.1 6.2 + - - +
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Residues in contact with LEU 106 (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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23H LEU* 4.0 18.4 - - + +
24H SER* 3.8 31.9 - - - +
25H GLN* 5.0 0.4 - - - -
28H ARG* 2.8 41.0 + - + +
60H HIS* 4.1 4.9 - - + -
61H ARG 3.7 9.4 - - - +
62H VAL* 4.1 10.3 - - + +
105H GLN* 1.3 73.5 - - - +
107H ARG* 1.3 64.5 + - - +
108H ALA 3.2 23.6 - - - +
109H GLY 3.4 20.7 - - - +
111H GLY* 4.0 11.7 - - - +
113H VAL* 3.7 22.2 - - + -
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Residues in contact with ARG 107 (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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53G GLU* 4.4 6.7 + - - -
114G PHE* 6.0 0.6 - - - -
61H ARG* 2.8 63.9 + - - +
63H GLU* 3.5 39.5 + - + +
77H PRO* 6.3 0.4 - - - +
105H GLN* 3.1 6.5 + - - -
106H LEU* 1.3 74.7 - - - +
108H ALA* 1.3 58.9 + - + +
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Residues in contact with ALA 108 (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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53G GLU* 3.7 38.8 - - + +
59H MET 3.8 9.6 - - - +
60H HIS* 3.1 2.6 - - - -
61H ARG* 3.0 28.3 + - + +
106H LEU* 3.2 10.9 - - - +
107H ARG* 1.3 80.5 - - - +
109H GLY* 1.3 62.8 + - - +
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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