Contacts of the helix formed by residues 102 - 110 (chain E) in PDB entry 5K58
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 ASN 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E PHE* 2.7 56.4 + - + +
99E GLY 2.8 4.0 + - - -
101E ARG* 1.3 88.6 - - - +
103E PRO* 1.3 65.4 - - - +
104E GLY 3.4 2.5 - - - -
105E LEU* 3.6 23.6 - - + +
106E THR* 3.0 25.8 + - - -
374N ILE* 5.2 0.2 - - - +
375N PRO 3.4 12.5 + - - +
376N ALA* 3.9 0.2 - - - -
377N PHE* 3.1 34.3 + - - +
378N LEU 4.7 1.0 + - - -
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Residues in contact with PRO 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLU* 3.3 38.8 - - + +
99E GLY 3.5 0.6 - - - +
100E GLU 4.2 4.9 - - - +
101E ARG 3.5 8.5 - - - +
102E ASN* 1.3 88.9 - - - +
104E GLY* 1.3 62.6 + - - +
106E THR* 3.3 9.2 + - - -
107E ARG* 3.4 6.9 + - - +
173E PHE* 3.7 15.9 - - + -
178E PHE* 3.1 43.5 - - + -
181E ARG* 4.5 7.4 - - - +
378N LEU* 5.9 2.2 - - + -
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Residues in contact with GLY 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ALA* 4.5 4.9 - - - -
23E LEU* 3.6 33.5 - - - +
24E GLU* 3.9 13.7 - - - +
102E ASN 3.4 0.4 - - - -
103E PRO* 1.3 79.1 - - - +
105E LEU* 1.3 67.6 - - - +
107E ARG* 3.1 17.5 + - - +
108E ILE* 3.5 9.2 - - - +
378N LEU* 5.9 2.3 - - - +
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ALA* 4.8 7.6 - - + -
23E LEU* 5.6 0.4 - - + -
62E LEU* 4.7 14.4 - - + +
65E PHE* 3.4 34.8 - - + -
66E ILE* 3.6 17.5 - - + +
98E PHE* 3.6 27.4 - - + -
102E ASN* 3.4 19.7 + - + +
103E PRO 3.4 0.4 - - - -
104E GLY* 1.3 76.1 - - - +
106E THR* 1.3 61.4 + - - +
107E ARG 3.3 0.2 - - - -
108E ILE* 3.3 13.8 - - - +
109E LEU* 3.0 28.0 + - - +
377N PHE* 4.0 28.5 - - + -
378N LEU* 5.6 3.1 - - + +
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Residues in contact with THR 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E PHE* 5.0 0.5 - - - -
99E GLY* 3.1 25.8 + - - -
102E ASN 3.0 17.7 + - - -
103E PRO 3.4 10.5 - - - -
104E GLY 3.1 0.4 - - - -
105E LEU* 1.3 77.4 - - - +
107E ARG* 1.3 55.2 + - - +
109E LEU* 2.9 10.2 + - + +
110E THR* 2.7 37.0 + - + -
170E LEU* 3.7 31.5 - - + +
173E PHE* 3.7 23.1 - - + -
174E VAL* 3.7 7.6 - - + -
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 2.8 31.3 + - + +
25E SER 3.3 18.4 + - - -
26E SER 5.0 0.4 + - - -
28E GLY* 3.9 15.2 + - - +
29E SER* 3.5 28.5 - - - +
103E PRO 3.4 2.6 + - - +
104E GLY 3.1 11.8 + - - +
106E THR* 1.3 79.3 - - - +
108E ILE* 1.3 55.5 + - - +
110E THR* 3.2 7.1 + - - +
112E HIS* 3.2 17.7 + - + -
113E ALA* 2.9 33.9 + - + +
174E VAL* 3.9 30.2 - - + +
177E GLU* 3.6 26.6 + - - -
178E PHE* 3.4 31.4 - - - -
115F MET* 5.5 3.4 - - + +
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Residues in contact with ILE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 4.7 2.7 - - + -
59E PHE* 5.2 6.5 - - + +
62E LEU* 4.5 20.4 - - + -
63E ILE* 3.4 21.8 - - + +
66E ILE* 4.1 13.7 - - + -
104E GLY 3.5 13.0 - - - +
105E LEU* 3.3 20.6 - - + +
107E ARG* 1.3 75.3 - - - +
109E LEU* 1.3 65.5 + - - +
111E GLY* 3.1 13.7 + - - +
113E ALA* 4.0 11.4 - - + -
114E LEU* 3.5 29.7 - - + +
125E ILE* 3.4 30.7 - - + +
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ILE* 4.3 21.5 - - + -
70E LEU* 4.6 9.6 - - + -
95E LEU 5.7 2.0 - - - +
98E PHE* 4.0 32.8 - - + -
105E LEU 3.0 11.9 + - - +
106E THR* 2.9 17.8 + - + +
108E ILE* 1.3 79.8 - - - +
110E THR* 1.3 63.0 - - + +
111E GLY* 4.2 0.3 - - - -
125E ILE* 3.4 30.6 - - + +
128E LEU* 4.8 8.1 - - + -
129E PHE* 3.6 43.4 - - + -
170E LEU* 4.7 17.5 - - + -
175F ARG* 5.3 0.5 - - - -
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Residues in contact with THR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E THR* 2.7 22.6 + - + +
107E ARG* 3.2 14.4 + - - -
109E LEU* 1.3 72.5 - - - +
111E GLY* 1.3 59.3 + - - +
112E HIS* 3.0 27.6 + - - -
129E PHE* 5.6 1.7 - - - -
167E GLU 5.6 0.9 - - - +
170E LEU* 3.1 40.8 - - + +
171E SER* 4.2 6.5 - - - +
174E VAL* 3.6 9.9 - - + +
112F HIS* 3.4 15.8 + - - -
171F SER* 5.8 3.1 - - - -
175F ARG* 5.0 11.1 - - - +
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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