Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 5EJC
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ALA 3.6 6.3 - - - +
102A THR* 1.3 95.6 - - + +
104A GLN* 1.3 64.8 + - - +
105A ALA* 3.3 4.9 - - + +
106A GLU* 3.1 28.5 + - + +
107A VAL* 3.0 19.1 + - - +
139A LYS* 6.4 1.6 - - - -
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TYR* 3.3 24.9 + - - -
89A LEU* 6.0 1.0 - - - +
102A THR 3.8 2.7 + - - +
103A PRO* 1.3 72.5 - - - +
105A ALA* 1.3 57.2 + - - +
107A VAL* 3.2 17.6 + - - +
108A TYR* 3.0 63.6 + - + +
142A GLU* 3.4 21.0 + - + +
148A SER* 4.3 7.5 + - - -
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PRO* 3.3 4.8 - - + +
104A GLN* 1.3 78.4 - - - +
106A GLU* 1.3 58.0 + - - +
108A TYR* 3.5 13.5 + - - +
109A LEU* 3.1 21.0 + - - +
135A LEU* 3.3 19.2 - - + +
138A ALA* 4.1 13.0 - - + +
139A LYS* 3.7 34.8 - - + -
142A GLU* 3.8 11.5 + - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE 5.6 1.4 - - - +
102A THR* 3.6 22.7 - - + +
103A PRO* 3.1 32.9 + - + +
105A ALA* 1.3 76.9 - - - +
107A VAL* 1.3 63.8 + - - +
109A LEU* 3.3 10.5 + - + +
110A ARG* 3.0 49.6 + - - +
123A PRO* 5.6 4.3 - - - +
127A LEU* 5.6 6.5 - - + -
135A LEU* 3.7 20.1 - - + +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TYR* 5.2 1.3 - - - +
89A LEU* 4.0 25.8 - - + -
92A LEU* 5.2 2.0 - - + -
98A VAL* 4.4 20.2 - - + -
99A SER 5.2 2.2 - - - +
102A THR* 4.3 20.6 - - - +
103A PRO 3.0 18.2 + - - +
104A GLN* 3.2 27.8 + - - +
106A GLU* 1.3 72.6 - - - +
108A TYR* 1.3 68.5 + - + +
110A ARG* 3.0 5.0 + - - +
111A MSE 2.9 36.7 + - + +
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Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TYR* 4.0 7.4 - - - -
104A GLN* 3.0 58.2 + - + +
105A ALA* 3.7 10.5 - - - +
107A VAL* 1.3 76.8 - - + +
109A LEU* 1.3 57.7 + - - +
111A MSE 3.3 9.9 + - - +
112A TYR* 2.9 30.1 + - - +
134A PHE* 3.6 13.0 - - + -
138A ALA* 4.4 11.4 - - + -
142A GLU* 4.5 9.5 - - + +
148A SER* 3.2 40.0 + - - -
151A CYS* 3.8 27.1 - - + +
152A TYR* 3.6 35.3 - + + -
155A THR* 5.2 2.5 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA 3.1 14.4 + - - +
106A GLU* 3.4 12.3 - - + +
107A VAL 3.1 0.2 - - - -
108A TYR* 1.3 74.9 - - - +
110A ARG* 1.3 74.8 + - - +
112A TYR* 3.1 8.6 + - + +
113A GLN* 2.8 51.0 + - + +
127A LEU* 4.0 27.8 - - + -
131A ASP* 4.2 25.6 - - + +
134A PHE* 3.4 29.1 - - + -
135A LEU* 4.1 14.8 - - + -
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.8 23.4 - - + +
97A PHE* 3.7 24.5 + - + +
98A VAL* 3.9 19.3 - - + -
106A GLU* 3.0 37.0 + - - +
107A VAL 3.0 7.0 + - - +
109A LEU* 1.3 88.8 - - - +
111A MSE 1.3 57.4 + - - +
113A GLN* 2.8 42.8 + - - +
114A LEU* 3.0 25.8 + - - +
119A LEU* 3.5 9.8 - - + +
120A PRO* 3.7 14.5 - - - +
122A SER 4.5 1.8 + - - -
123A PRO* 3.4 33.3 + - - +
125A PHE 4.7 4.9 + - - -
127A LEU* 5.2 12.7 - - - +
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Residues in contact with MSE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TYR* 3.2 64.6 - - + +
88A VAL* 3.6 26.2 - - + +
89A LEU* 4.0 6.1 - - - +
92A LEU* 3.6 17.3 - - + -
107A VAL* 2.9 32.6 + - + +
108A TYR* 3.5 9.4 - - - +
110A ARG* 1.3 75.0 - - - +
112A TYR* 1.3 57.4 + - - +
114A LEU* 3.3 2.6 + - - +
115A GLU* 2.9 34.2 + - - +
152A TYR* 3.5 29.4 - - + +
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR 2.9 17.7 + - - +
109A LEU* 3.4 9.0 - - + +
111A MSE 1.3 77.7 - - - +
113A GLN* 1.3 58.5 + - + +
115A GLU* 3.4 2.9 + - - +
116A SER* 2.6 56.4 + - - -
118A LYS* 4.2 18.5 + - - -
131A ASP* 6.0 1.3 - - - -
134A PHE* 3.4 40.2 - + + -
152A TYR* 3.6 10.5 + - + -
156A ARG* 3.8 35.2 - - + -
159A VAL* 4.2 10.1 - - + +
160A ASN* 5.1 9.6 + - + +
163A ASN* 3.8 20.4 + - - -
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 2.8 33.9 + - + +
110A ARG* 2.8 45.3 + - - +
112A TYR* 1.3 79.0 - - + +
114A LEU* 1.3 51.9 + - - +
116A SER* 3.4 5.4 + - - -
117A GLY 2.8 29.8 + - - -
118A LYS* 2.8 33.3 + - + +
119A LEU* 3.8 7.1 - - + +
120A PRO* 3.4 20.0 - - - +
131A ASP* 3.3 35.3 + - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 4.0 21.3 - - + +
91A ALA* 4.4 19.7 - - + -
92A LEU* 3.9 23.6 - - + -
95A VAL* 6.0 0.4 - - + -
110A ARG 3.0 17.1 + - - +
111A MSE 3.6 5.2 - - - +
113A GLN* 1.3 75.5 - - - +
115A GLU* 1.3 65.3 + - + +
117A GLY* 3.1 12.3 + - - -
119A LEU* 4.0 15.1 - - + +
950E ALA 4.6 0.4 - - - +
953E ARG* 3.6 24.1 - - + +
954E ILE* 3.9 23.6 - - + +
957E VAL* 3.8 31.9 - - + +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLN* 3.7 24.3 - - - +
88A VAL* 3.7 29.5 - - + +
111A MSE 2.9 19.5 + - - +
112A TYR* 3.9 3.4 - - - +
114A LEU* 1.3 78.8 - - + +
116A SER* 1.3 57.4 + - - +
152A TYR* 3.0 31.0 + - - +
153A TRP* 4.8 1.4 - - - -
156A ARG* 3.1 38.0 + - - +
950E ALA* 4.9 8.3 - - + +
953E ARG* 3.1 24.8 + - - +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR* 2.6 39.8 + - - -
113A GLN* 3.6 3.1 + - - -
115A GLU* 1.3 75.4 - - - +
117A GLY* 1.3 63.3 + - - +
118A LYS* 3.4 33.6 + - - +
156A ARG* 5.7 3.4 - - - -
953E ARG* 2.9 11.5 + - - +
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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