Contacts of the helix formed by residues 108 - 120 (chain C) in PDB entry 2AMT
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 HIS 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C VAL* 4.0 18.3 - - + +
24C ARG 4.9 1.7 + - - -
25C ILE* 3.4 36.9 - - + +
26C PRO* 4.2 13.8 - - + +
104C LYS 3.3 24.8 + - - -
105C MET 2.8 7.0 + - - +
107C PRO* 1.3 94.2 + - + +
109C ILE* 1.3 65.2 + - - +
110C PRO* 3.5 3.1 - - - -
111C GLN* 3.2 11.4 + - - +
112C MET* 3.2 35.8 + - + +
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Residues in contact with ILE 109 (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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56B ASP* 6.0 0.7 - - - +
59B LYS* 6.2 2.2 - - - +
98C ILE* 4.0 3.4 - - + -
105C MET* 3.1 38.5 + - + +
106C LEU* 3.6 14.6 - - + +
108C HIS* 1.3 74.2 - - - +
110C PRO* 1.4 74.1 - - + +
112C MET* 2.9 25.3 + - - +
113C ARG* 2.9 22.5 + - + +
129C VAL* 3.3 53.2 - - + +
130C LYS* 4.8 6.5 - - - -
131C ALA* 5.4 1.6 - - + +
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Residues in contact with PRO 110 (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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59B LYS* 6.0 4.3 - - - +
106C LEU 3.4 11.2 - - - +
107C PRO* 4.2 6.1 - - + +
108C HIS 3.6 4.7 - - - +
109C ILE* 1.4 95.5 - - + +
111C GLN* 1.3 56.2 + - - +
113C ARG* 3.4 13.3 - - + +
114C VAL* 3.1 32.5 + - + +
124C MET* 3.6 11.0 - - + +
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Residues in contact with GLN 111 (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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23C VAL* 3.6 18.4 - - + +
107C PRO 5.8 0.4 - - - +
108C HIS* 3.2 13.1 + - - +
109C ILE 3.1 0.6 - - - -
110C PRO* 1.3 78.8 - - - +
112C MET* 1.3 65.2 + - - +
114C VAL* 3.2 17.3 + - - +
115C PHE* 3.0 62.0 + - - -
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Residues in contact with MET 112 (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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20C ILE* 3.4 40.4 - - + +
21C GLY* 3.4 19.5 - - - +
23C VAL* 3.7 3.6 - - + -
25C ILE* 3.9 24.2 - - + -
40C ALA* 5.4 0.9 - - - -
98C ILE* 3.7 22.4 - - + -
105C MET* 4.3 3.8 - - - +
108C HIS* 3.3 19.5 - - + +
109C ILE* 2.9 30.8 + - + +
111C GLN* 1.3 76.1 - - - +
113C ARG* 1.3 57.6 + - - +
115C PHE* 3.3 2.8 + - - +
116C ILE* 2.8 37.9 + - + +
129C VAL* 4.0 13.9 - - + -
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Residues in contact with ARG 113 (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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53B ALA* 4.3 16.4 + - - +
59B LYS* 4.5 17.4 - - - +
109C ILE* 2.9 28.7 + - + +
110C PRO* 3.4 11.4 - - - +
112C MET* 1.3 76.6 - - - +
114C VAL* 1.3 51.5 + - - +
116C ILE* 3.4 1.4 + - - +
117C ALA* 2.8 38.1 + - - +
124C MET* 2.7 63.1 + - + +
125C ASP* 3.9 7.5 - - - +
127C VAL* 2.8 34.1 + - + +
128C ASN* 4.5 4.0 - - - +
129C VAL* 4.0 21.1 - - + +
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Residues in contact with VAL 114 (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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110C PRO* 3.1 18.1 + - + +
111C GLN* 3.2 22.9 + - - +
113C ARG* 1.3 74.3 - - - +
115C PHE* 1.3 61.9 + - + +
117C ALA* 3.2 7.0 + - - +
118C GLU* 2.9 51.0 + - + +
124C MET* 3.8 19.7 - - + -
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Residues in contact with PHE 115 (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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21C GLY 3.7 9.0 - - - +
22C GLY* 3.4 28.5 - - - -
23C VAL* 3.7 15.3 - - + -
41C LEU* 6.4 0.7 - - + -
74C ARG* 3.4 40.6 - - + +
111C GLN* 3.0 52.9 + - - +
112C MET 3.7 3.1 - - - +
114C VAL* 1.3 79.2 - - + +
116C ILE* 1.3 57.0 + - + +
118C GLU* 3.3 5.1 + - + +
119C ASP* 2.9 36.7 + - - +
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Residues in contact with ILE 116 (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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21C GLY* 4.9 2.9 - - - +
40C ALA* 6.0 2.9 - - + +
41C LEU* 3.8 28.3 - - + -
44C LEU* 3.6 30.7 - - + -
77C LEU* 4.7 2.0 - - + -
94C VAL* 4.4 2.0 - - + -
96C VAL* 4.8 6.1 - - + -
112C MET* 2.8 29.4 + - + +
113C ARG 3.8 2.9 - - - +
115C PHE* 1.3 72.5 - - - +
117C ALA* 1.3 57.6 + - - +
119C ASP* 3.4 5.4 + - - +
120C LEU* 2.9 40.9 + - + +
127C VAL* 3.7 23.8 - - + -
129C VAL* 3.9 26.5 - - + -
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Residues in contact with ALA 117 (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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113C ARG 2.8 21.1 + - - +
114C VAL* 3.2 7.2 + - - +
116C ILE* 1.3 75.0 - - - +
118C GLU* 1.3 61.7 + - + +
121C GLY* 3.0 6.6 + - - -
122C CYS* 2.9 53.0 + - - +
123C HIS 4.1 11.4 - - - +
124C MET* 4.1 13.9 - - + +
127C VAL* 4.2 2.7 - - + +
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Residues in contact with GLU 118 (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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74C ARG* 4.5 9.9 - - - +
78C ARG* 5.6 0.3 - - - -
114C VAL* 2.9 37.2 + - + +
115C PHE* 3.7 6.7 - - + +
117C ALA* 1.3 78.8 - - - +
119C ASP* 1.3 64.6 + - - +
121C GLY* 3.3 12.3 + - - -
122C CYS 5.4 1.2 - - - +
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Residues in contact with ASP 119 (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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41C LEU* 5.1 0.3 - - - +
74C ARG* 2.9 47.7 + - - +
77C LEU* 3.7 23.8 - - + +
78C ARG* 2.7 55.5 + - + +
81C TRP* 3.8 12.6 - - - -
115C PHE 2.9 19.9 + - - +
116C ILE 3.4 2.0 + - - +
118C GLU* 1.3 77.3 - - - +
120C LEU* 1.3 60.8 + - - +
121C GLY 3.8 0.2 + - - -
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Residues in contact with LEU 120 (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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44C LEU* 4.5 1.6 - - + -
48C LEU* 3.8 27.6 - - + -
77C LEU* 4.2 12.8 - - + -
81C TRP* 2.9 63.8 + - + +
85C GLN* 5.0 0.5 + - - -
91C LEU* 3.8 28.2 - - + +
94C VAL* 4.3 8.3 - - + -
116C ILE* 2.9 36.7 + - + +
119C ASP* 1.3 77.6 - - - +
121C GLY* 1.3 64.0 + - - +
122C CYS* 3.3 13.7 + - + +
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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