Contacts of the strand formed by residues 102 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A TRP 3.6 1.4 - - - +
31A THR* 3.2 1.5 - - - -
32A PHE* 2.7 51.9 + - + +
44A LEU* 4.4 5.6 - - + -
64A ILE* 3.6 24.5 - - + -
98A LEU* 3.8 37.9 - - + -
99A SER 3.9 13.5 - - - +
100A PRO* 4.0 7.4 - - + -
101A PRO* 1.3 76.2 - - - +
103A THR* 1.3 63.7 + - - +
104A PHE* 4.0 18.7 + - + -
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 3.7 25.8 - - + -
30A TRP 3.3 3.1 - - - +
31A THR* 2.9 28.9 + - - +
64A ILE* 3.3 9.0 - - - +
65A LEU* 2.9 59.2 + - + -
101A PRO* 5.3 1.9 - - - +
102A VAL* 1.3 77.3 - - - +
104A PHE* 1.3 63.5 - - - +
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TRP* 3.8 30.3 - + - -
23A LEU* 4.1 19.5 - - + -
28A ARG 3.8 0.4 - - - +
29A THR* 3.4 3.3 - - - -
30A TRP* 2.8 43.3 + + + +
32A PHE* 5.0 4.7 - - + -
44A LEU* 4.3 10.1 - - + -
46A LEU* 4.0 8.7 - - + -
62A VAL* 4.5 2.5 - - + -
63A GLU 3.3 6.5 - - - +
64A ILE* 4.0 15.5 - - + -
80A ILE* 3.9 24.7 - - + -
98A LEU* 3.9 19.1 - - + -
102A VAL* 4.0 19.7 - - + -
103A THR* 1.3 79.5 - - - +
105A GLN* 1.3 60.7 + - - +
115A LEU* 3.6 27.4 - - + -
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.3 4.7 - - - -
28A ARG* 2.9 22.3 + - - +
29A THR* 3.5 19.4 + - - +
62A VAL* 3.5 3.1 - - - +
63A GLU* 2.8 40.2 + - + +
65A LEU* 3.8 38.4 - - + +
104A PHE* 1.3 76.8 - - - +
106A LEU* 1.3 70.2 + - - +
107A ARG* 3.2 31.6 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.0 16.4 - - + +
24A SER* 3.8 32.3 - - - +
28A ARG* 2.5 60.1 + - + +
60A HIS* 4.3 2.2 - - + -
61A ARG 3.7 10.1 - - - +
62A VAL* 4.1 10.1 - - + +
105A GLN* 1.3 73.2 + - - +
107A ARG* 1.3 56.2 + - - +
108A ALA 3.4 17.5 - - - +
109A GLY 3.4 22.7 - - - +
111A GLY* 3.9 13.2 - - - +
113A VAL* 3.6 24.2 - - + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 4.4 4.5 + - - -
61A ARG* 2.9 49.4 + - - +
63A GLU* 3.5 41.5 + - + +
77A PRO* 5.4 5.6 - - - +
105A GLN* 3.2 33.7 + - + +
106A LEU* 1.3 73.8 - - - +
108A ALA* 1.3 60.3 + - + +
53B GLU* 4.8 0.2 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 4.9 1.1 - - - +
59A MET 3.9 7.4 - - - +
60A HIS* 3.3 2.6 - - - -
61A ARG* 3.1 30.1 + - + +
106A LEU* 3.4 11.8 - - - +
107A ARG* 1.3 78.8 - - + +
109A GLY* 1.3 62.2 + - - +
53B GLU* 3.6 39.7 - - + +
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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