Contacts of the helix formed by residues 103 - 117 (chain C) in PDB entry 1EFA
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 GLY 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C SER* 1.3 78.5 + - - +
104C VAL* 1.3 65.5 + - - -
105C GLU* 3.3 3.8 - - - -
106C ALA* 3.5 5.9 + - - +
107C CYS 3.4 14.0 + - - -
126C TYR* 2.9 23.7 + - - -
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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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103C GLY* 1.3 72.2 - - - -
105C GLU* 1.3 63.7 + - + +
107C CYS* 3.3 5.6 + - - +
108C LYS* 2.8 57.8 + - + +
128C LEU* 5.0 9.0 - - + -
132C ASP* 2.9 59.2 - - + +
136C VAL* 4.6 5.4 - - + -
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Residues in contact with GLU 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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103C GLY* 3.3 1.1 - - - -
104C VAL* 1.3 80.5 - - + +
106C ALA* 1.3 51.3 + - - +
108C LYS* 3.0 31.2 + - - +
109C THR* 2.7 40.3 + - - +
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Residues in contact with ALA 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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99C VAL* 3.5 12.2 - - + +
101C ARG* 3.4 62.1 + - + +
102C SER 4.7 1.1 - - - +
103C GLY* 3.5 8.6 + - - +
105C GLU* 1.3 80.1 - - - +
107C CYS* 1.3 57.7 + - - +
109C THR* 3.2 4.2 + - - -
110C ALA* 3.0 27.0 + - - +
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Residues in contact with CYS 107 (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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67C ALA* 4.8 5.2 - - - -
99C VAL* 4.0 11.3 - - - +
103C GLY 3.4 6.3 + - - +
104C VAL* 3.3 10.4 + - - +
105C GLU 3.2 0.6 - - - -
106C ALA* 1.3 78.3 - - - +
108C LYS* 1.3 58.3 + - - +
110C ALA* 3.3 1.9 + - - +
111C VAL* 2.9 36.4 + - - +
124C ILE* 3.9 27.4 - - - -
126C TYR* 3.9 33.2 - - + -
128C LEU* 4.1 12.6 - - + -
136C VAL* 4.3 10.1 - - + -
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Residues in contact with LYS 108 (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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104C VAL* 2.8 41.1 + - + +
105C GLU* 3.0 29.0 + - - +
107C CYS* 1.3 75.8 - - - +
109C THR* 1.3 65.3 + - - +
111C VAL* 3.1 8.4 + - - +
112C HIS* 2.8 24.4 + - - +
135C ALA* 4.1 26.0 - - - +
136C VAL* 4.3 14.6 - - + +
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Residues in contact with THR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG* 3.5 24.5 + - - +
105C GLU* 2.7 20.6 + - - +
106C ALA 3.4 8.5 - - - -
108C LYS* 1.3 73.3 - - - +
110C ALA* 1.3 61.6 + - - +
112C HIS* 3.1 19.4 + - + +
113C ASN* 3.1 27.9 + - - +
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Residues in contact with ALA 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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67C ALA* 4.3 7.4 - - + -
97C SER* 3.6 23.2 + - - +
98C MET 5.4 0.7 - - - +
99C VAL* 3.4 31.0 - - + -
106C ALA 3.0 6.5 + - - +
107C CYS* 3.4 9.0 - - - +
109C THR* 1.3 77.9 - - - +
111C VAL* 1.3 61.6 + - - +
113C ASN* 3.4 5.4 + - - +
114C LEU* 3.1 29.1 + - - +
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Residues in contact with VAL 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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67C ALA* 4.6 3.4 - - + -
107C CYS* 2.9 23.6 + - - +
108C LYS* 3.1 7.2 + - - +
110C ALA* 1.3 73.4 - - - +
112C HIS* 1.3 66.6 + - - +
114C LEU* 3.4 3.6 + - - +
115C LEU* 2.9 34.4 + - + +
122C LEU* 3.4 23.1 - - + -
124C ILE* 3.7 28.9 - - + -
136C VAL* 3.8 17.3 - - + -
139C ALA* 4.8 10.3 - - + -
140C CYS* 3.9 14.1 - - - -
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Residues in contact with HIS 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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108C LYS 2.8 13.2 + - - +
109C THR* 3.2 15.8 - - - +
111C VAL* 1.3 77.7 - - - +
113C ASN* 1.3 63.5 + - - +
115C LEU* 3.1 14.2 + - + +
116C ALA* 2.9 29.0 + - + +
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Residues in contact with ASN 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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97C SER* 4.4 9.6 + - - +
109C THR* 3.1 29.8 + - - +
110C ALA* 3.9 8.8 - - - +
112C HIS* 1.3 78.8 + - - +
114C LEU* 1.3 67.5 + - + +
116C ALA* 3.0 18.4 + - - +
117C GLN* 3.1 24.9 + - - +
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Residues in contact with LEU 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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65C GLY* 3.6 8.3 - - - -
66C VAL 3.2 39.9 - - - +
67C ALA* 3.6 11.9 - - + +
95C VAL* 4.5 4.3 - - + +
96C VAL 4.4 3.1 - - - -
97C SER* 3.2 35.7 - - - +
110C ALA 3.1 12.1 + - - +
111C VAL* 3.7 5.2 - - - +
113C ASN* 1.3 78.7 - - + +
115C LEU* 1.3 61.2 + - - +
117C GLN* 3.4 23.7 + - - +
119C VAL* 3.0 29.2 + - + +
122C LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 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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111C VAL* 2.9 27.0 + - + +
112C HIS* 3.2 15.5 - - + +
113C ASN 3.1 0.2 - - - -
114C LEU* 1.3 78.2 - - - +
116C ALA* 1.3 56.4 + - - +
117C GLN 3.1 0.2 - - - -
118C ARG* 2.7 38.0 + - - +
119C VAL* 4.4 5.8 - - + -
122C LEU* 4.1 18.8 - - + -
139C ALA* 3.3 27.8 - - + +
140C CYS* 4.1 2.2 - - - -
141C THR* 4.1 13.0 - - - +
143C VAL* 3.8 27.6 - - + -
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Residues in contact with ALA 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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112C HIS* 2.9 18.1 + - + +
113C ASN* 3.3 15.0 - - - +
115C LEU* 1.3 77.6 - - - +
117C GLN* 1.3 58.4 + - + +
118C ARG* 3.0 26.3 + - - +
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Residues in contact with GLN 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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55C GLN* 3.8 15.2 + - - +
63C LEU* 3.8 8.5 - - + +
95C VAL* 3.1 37.5 - - - +
113C ASN* 3.1 23.6 + - - +
114C LEU* 3.7 14.5 - - - +
115C LEU 3.1 1.6 - - - -
116C ALA* 1.3 75.8 - - + +
118C ARG* 1.3 70.4 + - - +
119C VAL* 3.4 6.6 + - + -
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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