Contacts of the helix formed by residues 104 - 114 (chain A) in PDB entry 5EWL
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A VAL* 3.9 23.1 - - + -
94A HIS* 4.2 10.8 - - + +
95A PRO* 4.6 5.1 - - + -
103A THR* 1.4 87.9 - - + +
105A THR* 1.4 50.4 + - - -
106A PRO* 3.5 0.9 - - - -
107A ILE* 3.0 18.5 + - + +
108A SER* 2.8 32.8 + - - -
120A GLY* 6.2 0.2 - - - -
123A THR* 3.1 32.3 - - + +
128A TYR* 3.5 20.6 - - + +
137A PHE* 4.3 15.7 - - + -
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Residues in contact with THR 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 THR* 3.0 11.8 + - - -
104A PRO* 1.4 75.6 - - - +
106A PRO* 1.4 60.8 - - + +
108A SER* 3.0 8.1 + - - -
109A TYR* 2.8 68.9 + - + +
128A TYR* 2.9 29.3 + - - -
134A HIS* 3.6 5.6 + - + -
114B PHE* 6.0 2.7 - - + -
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Residues in contact with PRO 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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71A ALA* 3.6 45.8 - - + +
74A MET* 4.4 8.5 - - + -
75A ALA* 4.2 13.9 - - + +
103A THR* 3.1 31.9 - - - +
105A THR* 1.4 81.3 - - + +
107A ILE* 1.3 57.0 + - + +
109A TYR* 4.1 5.0 - - + +
110A THR* 2.7 33.6 + - - -
114B PHE* 4.0 15.7 - - + -
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Residues in contact with ILE 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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32A VAL* 3.9 20.4 - - + -
67A HIS* 4.7 4.7 - - + -
74A MET* 4.0 18.2 - - + -
78A VAL* 4.0 27.2 - - + +
90A ILE* 3.9 20.4 - - + -
92A VAL* 3.4 49.4 - - + -
103A THR 4.6 2.5 - - - +
104A PRO* 3.0 15.1 + - + +
106A PRO* 1.3 74.9 - - - +
108A SER* 1.3 60.3 + - - +
110A THR* 3.9 0.7 - - - -
111A ALA* 2.9 34.1 + - - +
118A VAL* 4.3 6.7 - - + -
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Residues in contact with SER 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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104A PRO 2.8 15.6 + - - -
105A THR* 3.0 7.8 + - - -
107A ILE* 1.3 73.3 - - - +
109A TYR* 1.3 52.9 + - - -
111A ALA* 4.2 0.2 - - - +
112A GLY* 2.8 33.1 + - - -
118A VAL* 4.4 12.0 - - - +
133A ILE 4.5 0.4 + - - -
134A HIS* 2.6 45.1 + - - +
135A LEU* 5.1 2.3 - - - +
136A SER 5.8 0.7 + - - -
137A PHE* 3.9 18.8 - - - +
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Residues in contact with TYR 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 THR* 2.8 46.0 + - + +
106A PRO* 4.1 4.3 - - + +
108A SER* 1.3 72.8 - - - +
110A THR* 1.4 59.5 + - - +
112A GLY* 3.7 1.1 - - - -
113A PHE* 2.9 31.2 + - - +
133A ILE* 3.8 40.1 - - + +
134A HIS* 3.9 10.4 + + - -
135A LEU* 6.1 1.1 - - + -
110B GLN* 3.9 42.7 + - + -
114B PHE* 4.9 20.4 - + + -
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Residues in contact with THR 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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75A ALA* 3.8 21.4 - - - +
78A VAL* 3.8 22.2 - - + -
79A CYS* 3.6 30.3 - - - -
83A ILE* 4.0 4.9 - - + -
106A PRO 2.7 24.8 + - - -
107A ILE 4.0 1.8 - - - -
109A TYR* 1.4 74.5 - - - +
111A ALA* 1.3 61.7 + - - +
113A PHE* 3.3 18.6 - - - +
114A TYR* 3.4 12.3 - - - -
329A CYS* 4.2 2.5 - - - -
78B PRO* 4.6 15.0 - - + +
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Residues in contact with ALA 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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78A VAL* 4.8 0.4 - - - +
83A ILE* 4.6 7.8 - - - +
90A ILE* 3.9 19.5 - - + -
107A ILE 2.9 18.0 + - - +
110A THR* 1.3 72.7 - - - +
112A GLY* 1.3 60.7 + - - +
114A TYR* 3.1 5.0 + - - +
115A ARG 3.0 7.6 + - - -
116A ILE* 2.9 48.2 + - + +
118A VAL* 3.5 18.2 - - + -
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Residues in contact with GLY 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 SER 2.8 20.8 + - - -
109A TYR 3.3 1.3 + - - -
111A ALA* 1.3 73.6 - - - +
113A PHE* 1.3 58.6 + - - +
115A ARG* 2.9 38.1 + - - -
116A ILE 4.3 2.6 + - - -
118A VAL* 5.5 0.2 - - - +
135A LEU* 3.8 25.0 - - - +
136A SER* 5.0 6.1 - - - -
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Residues in contact with PHE 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 TYR 2.9 13.0 + - - +
110A THR 3.3 12.6 - - - +
112A GLY* 1.3 76.7 - - - +
114A TYR* 1.4 94.2 + + - +
115A ARG* 3.9 4.7 + - - +
332A ASN 3.6 6.3 - - - -
333A THR* 4.0 21.6 - - + +
334A ASN 5.3 0.3 - - - -
335A ILE* 3.6 19.6 + - - +
77B ASP* 4.2 0.7 - - - -
78B PRO* 3.6 30.5 - - + -
105B GLN* 3.8 27.8 - - + -
107B ALA* 4.0 26.0 - - + -
111B ILE* 4.2 8.7 - - + -
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Residues in contact with TYR 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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83A ILE* 3.8 15.0 - - + -
110A THR 3.4 22.4 - - - -
111A ALA 3.1 3.2 + - - +
113A PHE* 1.4 93.1 - + - +
115A ARG* 1.4 65.4 + - - +
116A ILE* 3.3 18.6 - - + -
326A PRO* 3.5 23.3 - - + -
328A GLY 4.5 1.3 - - - -
329A CYS* 3.1 48.7 + - - +
332A ASN* 2.8 41.6 + - + -
334A ASN 3.6 12.6 - - - -
335A ILE* 4.2 3.8 - - - +
336A TRP* 2.8 33.3 + - - +
78B PRO* 3.7 9.7 - - + +
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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