Contacts of the strand formed by residues 104 - 108 (chain D) in PDB entry 3L3T
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 MET 104 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 4.2 11.4 - - + -
53D VAL* 3.6 5.5 - - - +
54D SER* 2.9 46.7 + - - +
55D ALA 3.2 31.0 - - - +
56D ALA* 3.8 2.5 - - - -
58D CYS 4.0 17.3 - - - +
59D TYR* 3.7 23.6 - - - -
63D ILE* 4.8 1.6 - - + -
88D ILE* 3.7 20.9 - - + -
89D ILE 3.5 17.3 - - - +
90D ARG* 4.1 4.5 - - - +
91D HIS 4.6 0.2 - - - +
103D ILE* 1.3 79.3 - - - +
105D LEU* 1.3 75.0 + - - +
106D ILE* 4.4 11.0 - - + -
237D TRP* 4.7 1.6 - - - -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 4.2 11.2 - - + -
51D TRP* 4.0 25.1 - - + -
52D VAL 3.5 16.2 - - - +
53D VAL* 3.7 23.6 - - + -
87D LYS 3.9 0.2 - - - +
89D ILE* 2.8 43.4 + - + +
103D ILE* 6.1 0.4 - - + -
104D MET* 1.3 75.9 - - - +
106D ILE* 1.3 65.1 + - - +
237D TRP* 3.5 31.1 - - + -
238D ILE* 3.7 30.1 - - + +
241D THR* 4.0 16.6 - - + -
242D ILE* 4.9 0.4 - - + -
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 4.3 26.9 - - + -
50D GLN 3.5 0.3 - - - +
51D TRP* 3.3 12.5 - - - -
52D VAL* 2.9 42.6 + - + +
54D SER* 5.5 1.8 - - - -
63D ILE* 4.2 26.7 - - + -
65D VAL* 4.3 12.8 - - + -
85D ALA* 3.7 28.3 - - + -
87D LYS 3.2 7.9 - - - +
88D ILE* 4.3 11.9 - - + -
104D MET* 4.4 9.6 - - + -
105D LEU* 1.3 79.9 - - - +
107D LYS* 1.3 68.9 + - - +
108D LEU* 3.9 5.1 + - + +
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Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLN* 3.3 38.7 - - + +
51D TRP* 3.6 36.4 - - + +
85D ALA* 3.5 1.9 - - - -
86D ALA* 2.6 39.1 + - + -
87D LYS* 2.8 41.0 + - + +
106D ILE* 1.3 75.2 - - - +
108D LEU* 1.3 63.7 + - - +
245D ASN 2.9 24.5 + - - +
246D SER* 4.0 13.1 + - - +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.1 19.3 - - + -
49D GLU 3.7 20.6 - - - +
50D GLN* 2.8 37.5 + - - +
51D TRP* 5.1 0.2 - - - -
52D VAL* 4.2 11.4 - - + -
65D VAL* 3.9 34.5 - - + -
67D LEU* 4.6 4.5 - - + -
83D ILE* 3.7 18.4 - - + -
84D ASN 3.7 4.7 - - - +
86D ALA* 4.2 0.9 - - - +
106D ILE* 4.3 4.0 - - + -
107D LYS* 1.3 83.0 - - - +
109D SER* 1.3 59.2 + - - +
110D SER 3.1 20.9 - - - +
112D ALA* 4.2 11.2 - - + -
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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