Contacts of the strand formed by residues 101 - 106 (chain C) in PDB entry 3TQS
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 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C THR* 3.7 32.8 - - + +
37C VAL* 4.0 22.7 - - + -
92C PHE* 3.3 41.5 - - + +
95C VAL* 3.8 18.2 - - + +
97C THR* 3.8 20.0 - - + -
99C LYS 4.6 0.9 - - - +
100C PRO* 1.3 72.8 - - - +
102C ARG* 1.3 63.1 + - - +
103C VAL* 3.7 8.8 + - + +
125C CYS* 2.7 21.5 + - + +
126C ILE* 3.5 6.2 - - + +
127C GLU 2.7 24.9 + - - -
128C ASP 3.8 0.5 + - - -
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Residues in contact with ARG 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 2.8 44.0 + - + +
29C HIS 3.3 9.9 + - - -
30C PRO* 3.8 0.8 - - - +
31C GLN* 5.9 0.6 + - - -
34C ASP* 3.0 40.3 + - + -
35C THR 2.9 13.8 + - - +
36C LEU* 3.1 22.2 - - + +
37C VAL 2.9 22.9 + - - -
100C PRO 4.9 0.9 - - - +
101C LEU* 1.3 71.6 - - - +
103C VAL* 1.3 61.6 + - - +
104C VAL* 4.7 2.9 - - + -
127C GLU* 3.5 30.2 + - - +
128C ASP* 2.8 42.4 + - - +
130C HIS* 3.8 12.1 - - - -
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 3.4 17.5 - - + +
39C ILE* 3.7 20.4 - - + -
92C PHE* 4.8 6.7 - - + -
101C LEU* 4.3 10.5 - - + +
102C ARG* 1.3 71.9 - - - +
104C VAL* 1.3 70.1 + - - +
119C LEU* 4.5 8.7 - - + -
126C ILE* 4.2 33.0 - - + -
128C ASP* 3.0 6.7 + - - +
129C MSE 3.2 14.9 - - + -
130C HIS* 3.0 23.2 + - - -
131C PHE* 3.7 23.8 - - + -
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 3.7 33.4 - - + -
36C LEU* 4.4 17.0 - - + -
37C VAL 2.9 18.6 + - - +
38C GLU* 3.7 21.5 - - + -
39C ILE* 2.8 22.3 + - - +
46C LEU* 4.8 4.7 - - + -
50C LEU* 4.2 17.0 - - + -
102C ARG* 4.4 4.0 - - + +
103C VAL* 1.3 83.2 - - - +
105C GLY* 1.3 60.5 + - - +
130C HIS* 3.1 17.0 - - + +
131C PHE* 3.7 9.9 - - - -
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Residues in contact with GLY 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLU* 4.5 7.0 - - - -
39C ILE* 3.0 13.2 - - - -
40C GLY 5.2 0.4 - - - -
46C LEU* 5.5 5.3 - - - +
104C VAL* 1.3 81.9 - - - +
106C ASN* 1.3 55.9 + - - +
130C HIS 3.2 5.7 + - - +
131C PHE* 3.3 14.9 - - - -
132C MSE 2.8 31.2 + - - +
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Residues in contact with ASN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C HIS* 3.0 28.2 + - - +
14C PHE* 5.0 0.4 - - - +
15C LEU* 4.7 8.8 - - - +
39C ILE 3.0 9.6 + - - +
40C GLY* 3.8 24.4 + - - +
105C GLY* 1.3 73.4 - - - +
107C LEU* 1.3 70.4 + - - +
108C PRO* 4.0 5.4 - - - +
132C MSE 3.6 27.6 - - + +
174C PHE* 4.2 11.6 - - - -
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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