Contacts of the strand formed by residues 114 - 118 (chain A) in PDB entry 1TF4
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 LEU 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 4.7 3.6 - - + +
107A ALA* 3.5 21.1 - - + +
108A HIS* 4.3 7.6 - - + -
112A ASN 4.2 0.2 - - - -
113A VAL* 1.3 74.3 - - - +
115A TYR* 1.3 65.6 + - - +
116A VAL* 3.4 20.9 + - + -
142A LYS* 3.3 3.7 - - - -
143A VAL* 2.9 45.2 + - + +
152A VAL* 4.1 2.2 - - + +
153A ALA* 3.8 25.4 - - + +
156A THR* 3.7 32.5 - - + +
185A LEU* 4.0 24.0 - - + -
188A PHE* 4.8 3.3 - - + -
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.8 33.7 + - + +
47A LEU* 3.4 30.7 - - + +
49A LEU* 3.8 26.7 - - + -
63A GLY* 5.7 0.5 - - - -
103A TYR* 4.8 8.5 + - - +
107A ALA* 2.9 40.3 + - + +
109A PRO* 4.2 5.8 - - + -
113A VAL* 4.1 16.5 - - + +
114A LEU* 1.3 74.4 - - - +
116A VAL* 1.3 59.7 + - - +
117A GLN 3.7 3.1 - - - +
118A VAL* 5.8 0.4 - - + -
140A SER* 4.0 11.2 - - - -
141A PHE 3.3 18.6 - - - +
142A LYS* 3.6 30.1 + - + +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS 4.3 0.4 - - - -
62A PHE* 4.2 0.3 - - - -
63A GLY* 2.8 32.6 + - - -
64A PHE 4.6 0.5 + - - -
103A TYR* 5.5 2.0 - - - -
114A LEU* 3.6 25.6 - - + +
115A TYR* 1.3 74.1 - - - +
117A GLN* 1.3 62.9 + - + +
141A PHE 3.0 5.9 + - - +
142A LYS* 4.4 0.7 - - - -
143A VAL* 4.0 8.7 - - + -
152A VAL* 3.6 39.9 - - + -
196A TYR* 4.2 10.7 - - + -
200A VAL* 3.6 40.2 - - + -
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Residues in contact with GLN 117 (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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60A VAL* 4.1 7.2 - - + +
61A LYS 3.3 12.8 - - - +
62A PHE* 3.7 19.4 - - + -
103A TYR* 5.2 1.2 + - - -
115A TYR* 3.7 2.5 - - - -
116A VAL* 1.3 85.3 - - + +
118A VAL* 1.3 69.0 + - - +
119A GLY 2.9 23.0 + - - +
120A ASP* 4.4 0.6 + - - +
121A GLY 4.3 7.5 - - - +
139A PRO 3.9 0.2 - - - +
140A SER* 3.5 2.3 - - - -
141A PHE* 2.8 57.3 + - + +
196A TYR* 5.6 0.6 - - + -
200A VAL* 4.2 4.5 - - + +
201A PRO* 4.0 17.5 + - - +
202A ALA* 3.4 30.3 + - - +
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Residues in contact with VAL 118 (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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41A ASP* 3.5 38.8 - - + +
49A LEU* 4.0 28.9 - - + -
60A VAL* 3.7 2.6 - - - +
61A LYS* 3.0 42.6 + - + +
103A TYR* 3.5 20.2 - - - +
115A TYR* 5.8 1.1 - - + -
117A GLN* 1.3 78.8 - - - +
119A GLY* 1.3 63.7 + - - +
138A ARG* 3.9 16.1 + - + +
139A PRO 3.5 6.7 - - - +
140A SER* 4.5 4.9 - - - +
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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