Contacts of the helix formed by residues 125 - 137 (chain F) in PDB entry 3DLL
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 ALA 125 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F TRP* 6.3 3.6 - - + -
105F VAL* 3.8 14.7 - - + +
106F LEU* 6.0 3.6 - - + -
121F VAL* 3.7 14.6 - - + +
122F GLU 5.4 1.6 - - - -
123F ALA 2.8 10.5 + - - +
124F ALA* 1.3 75.1 - - - +
126F ASN* 1.3 60.2 + - - +
127F THR 4.1 0.2 - - - +
128F VAL* 2.9 15.8 - - - +
129F ALA* 2.4 30.9 + - - +
133F ARG* 5.2 0.3 + - - -
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Residues in contact with ASN 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F GLU 5.6 4.2 + - - -
123F ALA 3.7 2.4 + - - +
125F ALA* 1.3 79.9 - - - +
127F THR* 1.3 62.6 + - - +
128F VAL 2.8 5.3 + - - -
129F ALA* 3.3 12.1 + - + +
130F GLY 3.4 10.6 + - - -
133F ARG* 3.5 24.3 + - - -
1090X C 3.6 8.5 + - - +
1091X C 3.2 43.0 + - - +
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Residues in contact with THR 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F LEU* 3.2 35.7 - - + +
123F ALA 3.7 2.7 + - - -
126F ASN* 1.3 76.6 - - - +
128F VAL* 1.3 60.3 + - - +
131F THR* 3.3 9.9 + - - -
1069X G 3.1 17.5 - - - +
1070X G 2.6 34.1 + - - +
1091X C 2.4 54.3 + - - +
1092X U 3.4 14.6 + - - -
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Residues in contact with VAL 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F VAL* 3.1 26.5 - - + -
108F ILE* 5.6 8.5 - - + -
109F ALA* 4.8 6.1 - - + +
116F LEU* 4.0 13.7 - - + -
124F ALA* 3.4 12.1 - - + +
125F ALA* 2.9 31.4 - - - +
127F THR* 1.3 78.8 - - - +
129F ALA* 1.3 67.6 + - - +
131F THR* 3.0 10.7 + - - -
132F ALA* 2.9 28.6 + - + -
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F VAL* 6.2 1.6 - - - -
125F ALA 2.4 27.4 + - - +
126F ASN* 3.4 15.7 - - + +
128F VAL* 1.3 69.0 - - - +
130F GLY* 1.3 69.7 + - - +
132F ALA* 2.9 3.3 + - - -
133F ARG* 2.8 70.6 + - - +
139F VAL* 5.8 2.0 - - + -
1090X C 5.2 1.6 - - - +
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Residues in contact with GLY 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ASN 3.4 7.9 + - - -
128F VAL 3.3 0.2 + - - -
129F ALA* 1.3 80.7 - - - +
131F THR* 1.3 63.7 + - - +
133F ARG* 4.4 4.9 - - - +
134F SER* 3.1 16.2 + - - -
1090X C 3.9 24.0 + - - -
1099X A 3.1 26.8 + - - -
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Residues in contact with THR 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ARG* 5.2 15.7 - - - +
127F THR 3.3 15.9 + - - -
128F VAL* 3.0 11.8 + - - -
129F ALA 2.9 0.4 + - - -
130F GLY* 1.3 76.1 - - - +
132F ALA* 1.3 66.4 + - - +
134F SER 4.1 1.2 - - - -
135F MET* 3.4 21.2 + - + +
1070X G 4.2 2.2 + - - +
1071X U 2.5 41.2 + - + +
1073X G 4.6 13.9 + - - +
1099X A 3.8 3.6 - - - +
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ARG* 5.9 9.0 - - + -
105F VAL* 5.7 3.8 - - + -
128F VAL* 2.9 25.4 + - + +
129F ALA* 2.9 9.3 + - - +
131F THR* 1.3 76.0 - - - +
133F ARG* 1.3 65.5 + - - +
135F MET* 3.1 10.5 - - - +
137F VAL* 2.9 42.2 - - + +
139F VAL* 4.7 5.6 - - + -
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Residues in contact with ARG 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ASN* 4.3 11.8 + - - +
102F TRP* 5.2 4.4 - - - -
125F ALA 5.2 0.6 + - - -
126F ASN* 3.5 15.2 + - - -
129F ALA* 2.8 50.2 + - - +
130F GLY* 4.0 3.9 - - - +
132F ALA* 1.3 74.9 - - - +
134F SER* 1.3 53.7 + - - +
135F MET 2.7 12.3 + - - -
136F GLY* 3.1 10.6 + - - -
137F VAL* 3.2 21.1 + - - +
139F VAL* 3.9 34.5 - - + +
140F GLU 4.6 12.7 + - - -
1090X C 5.4 6.5 + - - -
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Residues in contact with SER 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F PRO* 3.3 12.3 - - - +
93F ASN* 3.8 19.1 + - - +
130F GLY 3.1 16.2 + - - -
131F THR 4.1 2.9 - - - -
133F ARG* 1.3 72.8 - - - +
135F MET* 1.3 56.9 + - - +
1073X G 2.6 39.5 + - - +
1074X G 4.5 8.0 - - - -
1087X C 3.2 11.1 + - - +
1088X A 3.8 16.9 - - - -
1099X A 4.0 6.3 - - - -
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Residues in contact with MET 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ARG* 3.9 28.7 - - - +
81F LYS* 6.0 1.3 - - - +
83F ALA 5.2 6.7 - - - +
84F GLY* 5.6 1.3 - - - -
85F ILE* 3.8 30.1 - - + +
89F SER* 2.6 31.9 - - - +
92F PRO* 3.0 13.7 - - - +
131F THR* 3.4 14.1 - - + +
132F ALA* 3.1 16.4 - - - +
133F ARG 2.7 3.0 + - - -
134F SER* 1.3 74.0 - - - +
136F GLY* 1.3 50.4 + - - +
137F VAL* 4.6 4.9 - - + -
1073X G 4.4 4.5 - - - +
1074X G 2.9 55.2 - - - +
1075X C 4.7 0.7 - - - +
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Residues in contact with GLY 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F SER* 3.2 13.0 + - - -
92F PRO* 3.2 17.4 - - - +
93F ASN 5.2 0.9 - - - -
96F LYS* 6.0 0.2 - - - -
97F VAL 5.1 0.8 + - - -
98F GLY* 2.8 38.1 + - - +
133F ARG 3.1 2.1 + - - -
135F MET* 1.3 81.6 - - - +
137F VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ARG* 6.1 4.0 - - + -
98F GLY 3.9 2.2 - - - -
100F LEU* 4.6 26.5 - - + -
132F ALA* 2.9 42.6 - - + +
133F ARG* 3.2 16.4 + - - +
135F MET* 4.6 4.5 - - + -
136F GLY* 1.3 83.0 - - - +
138F THR* 1.3 69.4 + - - +
139F VAL* 3.4 26.3 + - + -
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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