Contacts of the helix formed by residues 112 - 124 (chain B) in PDB entry 4TTB
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 PRO 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.6 38.1 - - + +
86A MET* 4.7 4.3 - - + -
87A VAL* 5.1 2.0 - - + -
110B GLN 4.2 2.7 - - - +
111B VAL* 1.3 85.9 - - + +
113B MET* 1.3 66.5 + - - +
114B GLU* 4.5 3.6 - - + +
115B VAL* 3.0 43.8 + - + +
116B ILE* 3.3 6.6 + - - +
267B TYR* 3.8 17.3 - - - +
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Residues in contact with MET 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A MET* 4.3 9.6 - - + -
288A THR* 3.5 33.4 - - + +
111B VAL 3.2 5.9 + - - +
112B PRO* 1.3 67.7 - - - +
114B GLU* 1.3 61.0 + - - +
116B ILE* 3.1 22.8 + - + +
117B ASP* 2.9 56.0 + - - +
139B VAL* 4.8 4.7 - - + -
141B LYS* 4.3 29.6 - - + +
190B ILE* 5.9 1.1 - - - -
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.3 37.4 - - + +
91A GLN* 5.1 3.3 - - - +
112B PRO* 3.1 4.7 - - + +
113B MET* 1.3 78.9 - - - +
115B VAL* 1.3 59.4 + - + +
117B ASP* 3.2 14.2 + - + +
118B ASN* 2.9 38.2 + - - +
121B ARG* 6.2 0.2 - - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MET* 3.7 27.8 - - + -
87A VAL* 3.8 34.5 - - + +
90A SER* 4.2 11.4 - - - +
112B PRO* 3.0 33.3 + - + +
114B GLU* 1.3 76.4 - - - +
116B ILE* 1.3 61.7 + - + +
118B ASN* 3.2 2.3 + - - +
119B VAL* 3.2 23.8 + - + +
231B ALA* 4.2 13.5 - - + -
233B LEU* 4.0 16.8 - - + -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 3.5 36.8 - - + -
112B PRO 3.7 7.6 - - - +
113B MET* 3.1 27.5 + - + +
115B VAL* 1.3 74.4 - - - +
117B ASP* 1.3 66.0 + - - +
119B VAL* 3.5 9.3 + - + +
120B ILE* 3.2 41.2 + - + +
139B VAL* 4.4 17.0 - - + -
190B ILE* 4.9 8.3 - - + -
192B ILE* 4.8 7.4 - - + -
233B LEU* 4.2 19.1 - - + -
265B VAL* 4.2 13.0 - - + -
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 3.6 18.9 - - + +
286A MET* 3.6 13.0 - - - +
113B MET* 2.9 44.9 + - - +
114B GLU* 3.3 14.3 - - - +
116B ILE* 1.3 78.5 - - - +
118B ASN* 1.3 57.0 + - - +
120B ILE* 3.2 5.3 + - - +
121B ARG* 2.8 52.4 + - - +
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.9 2.8 + - - +
90A SER* 3.2 36.1 + - - +
91A GLN* 3.6 27.2 - - - +
94A TYR* 4.1 7.4 - - + +
114B GLU* 2.9 35.3 + - - +
115B VAL 3.2 3.1 + - - +
116B ILE 3.2 0.4 - - - -
117B ASP* 1.3 78.9 - - - +
119B VAL* 1.3 52.0 + - - +
121B ARG* 3.1 28.1 + - - +
122B THR* 2.7 37.6 + - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 4.6 6.7 - - - -
115B VAL* 3.2 18.4 + - + +
116B ILE* 3.5 15.7 - - + +
118B ASN* 1.3 76.3 - - - +
120B ILE* 1.3 68.2 + - + +
122B THR* 3.5 2.4 + - - -
123B ALA* 3.0 25.6 + - - +
192B ILE* 5.0 4.5 - - + -
224B LEU* 3.7 22.7 - - + +
227B ALA* 3.7 41.7 - - + +
228B LEU* 4.0 17.3 - - + +
231B ALA* 4.4 13.5 - - + -
233B LEU* 5.2 0.9 - - + -
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LEU* 3.9 18.2 - - + -
285A ILE* 3.5 9.4 - - + +
286A MET* 4.1 15.5 - - + -
116B ILE* 3.2 24.4 + - + +
117B ASP* 3.8 3.8 - - - +
119B VAL* 1.3 83.0 - - + +
121B ARG* 1.3 64.9 + - - +
123B ALA* 3.1 6.9 + - - +
124B GLY 3.0 17.7 + - - -
137B PHE* 3.9 36.6 - - + -
139B VAL* 3.5 31.9 - - + -
192B ILE* 4.3 11.9 - - + -
224B LEU* 4.6 4.7 - - + -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 3.7 40.9 - - + -
282A LEU* 3.7 42.0 - - + +
285A ILE* 4.6 4.0 - - - -
114B GLU* 6.2 0.4 - - - +
117B ASP* 2.8 32.9 + - - +
118B ASN* 3.1 29.2 + - - +
120B ILE* 1.3 74.9 - - - +
122B THR* 1.3 63.7 + - - +
124B GLY* 2.9 13.5 + - - -
125B THR* 3.3 13.0 + - - +
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER 4.3 2.3 + - - -
93A PHE* 3.8 19.7 - - + +
94A TYR* 3.2 21.7 + - - +
97A LEU* 3.4 33.0 - - + -
118B ASN 2.7 23.0 + - - -
119B VAL* 3.5 9.0 - - - -
120B ILE 3.2 0.2 - - - -
121B ARG* 1.3 77.2 - - - +
123B ALA* 1.3 58.5 + - - +
125B THR* 2.9 32.7 + - - -
223B ILE* 3.5 10.5 - - + +
227B ALA* 4.2 5.2 - - + +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL 3.0 14.7 + - - +
120B ILE* 3.1 9.8 + - - +
122B THR* 1.3 77.5 - - - +
124B GLY* 1.3 59.0 + - - +
125B THR 3.0 4.6 + - - -
126B ALA* 3.2 22.0 + - - +
137B PHE* 3.7 22.0 - - + -
220B ALA* 3.5 25.6 - - - +
223B ILE* 3.9 11.6 - - - +
224B LEU* 3.9 12.1 - - + +
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ARG* 3.9 13.7 - - - +
285A ILE* 3.8 21.7 - - - +
120B ILE 3.0 6.1 + - - -
121B ARG 2.9 12.2 + - - -
123B ALA* 1.3 73.6 - - - +
125B THR* 1.3 57.7 + - - +
126B ALA 3.2 5.0 + - - +
133B GLU* 4.2 6.9 - - - +
135B TRP* 3.6 25.6 + - - -
137B PHE* 5.0 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