Contacts of the strand formed by residues 99 - 103 (chain A) in PDB entry 4TZ1
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 TYR 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASN* 3.6 11.7 - - - +
69A LEU* 4.0 23.1 - - + -
85A VAL* 3.9 25.4 - - + -
88A LYS* 3.2 33.0 + - - -
89A GLN* 3.5 42.2 - - + -
97A ASP* 2.7 38.2 + - + -
98A ARG* 1.3 83.8 - - - +
100A ALA* 1.3 60.0 + - - +
101A LEU* 4.7 6.3 - - + -
118A TYR 3.1 9.4 + - - +
119A THR* 3.3 9.7 - - + +
120A SER 3.0 23.1 + - - -
355A GLY* 3.3 10.7 + - - -
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Residues in contact with ALA 100 (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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67A ASN 2.9 8.4 + - - +
68A VAL* 3.5 12.5 - - + +
69A LEU* 2.9 28.4 + - - +
99A TYR* 1.3 73.9 - - - +
101A LEU* 1.3 66.1 + - - +
102A MET* 4.8 10.8 - - + -
120A SER* 3.3 18.8 - - - +
333A PRO* 3.8 18.5 - - + +
354A LEU* 4.2 8.3 - - + -
355A GLY 3.9 4.7 - - - +
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Residues in contact with LEU 101 (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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69A LEU* 3.5 29.4 - - + +
71A PHE* 4.5 8.3 - - + -
81A LYS 5.4 0.4 - - - +
82A VAL* 4.1 28.5 - - + +
85A VAL* 4.4 19.1 - - + -
99A TYR* 4.7 3.6 - - + -
100A ALA* 1.3 79.2 - - - +
102A MET* 1.3 61.7 + - - +
103A PHE* 4.0 17.3 - - + -
114A GLN 5.8 0.4 - - - +
115A ILE* 4.5 12.8 - - + -
119A THR* 3.8 22.7 - - + -
120A SER 2.8 16.3 + - - +
121A ILE* 3.2 8.6 - - + +
122A ALA 2.9 26.5 + - - +
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Residues in contact with MET 102 (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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68A VAL* 4.0 20.0 - - + -
69A LEU 2.9 10.5 + - - +
70A VAL* 3.4 10.9 - - + +
71A PHE* 2.9 26.7 + - - +
100A ALA* 4.8 8.7 - - + -
101A LEU* 1.3 75.3 - - - +
103A PHE* 1.3 65.4 + - - +
104A LYS 4.2 0.2 - - - -
120A SER* 5.5 3.1 - - - +
122A ALA* 3.4 28.5 - - + +
123A GLY 4.9 0.4 - - - +
124A LEU* 3.8 32.5 - - + -
269A LEU* 4.1 22.4 - - + +
276A TYR* 6.4 0.2 - - + -
354A LEU* 3.8 29.8 - - + -
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Residues in contact with PHE 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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71A PHE* 3.6 28.3 - + + -
78A ILE* 4.2 6.7 - - + -
82A VAL* 4.1 14.4 - - + -
101A LEU* 4.0 12.6 - - + -
102A MET* 1.3 77.4 - - - +
104A LYS* 1.3 64.5 + - - +
108A TYR* 3.8 20.0 - + - +
111A ILE* 3.9 15.5 - - + -
121A ILE* 3.5 32.3 - - + -
122A ALA 2.9 19.4 + - - +
123A GLY* 3.5 1.6 - - - -
124A LEU* 2.9 31.5 + - - +
131A THR* 3.7 19.2 - - + +
133A PHE* 3.6 31.9 - + + -
159A LEU* 4.7 0.2 - - + -
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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