Contacts of the helix formed by residues 111 - 125 (chain B) in PDB entry 5JLH
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ILE* 3.5 24.9 - - + -
106B GLU* 4.1 3.3 - - - +
109B LEU 3.8 2.7 - - - +
110B ASN* 1.3 101.7 - - - +
112B LYS* 1.3 66.6 + - - +
113B ALA* 3.2 9.6 - - + +
114B ASN* 3.3 18.3 + - - +
115B ARG* 3.8 3.5 + - - -
176B ARG* 3.9 5.4 - - - +
193D THR* 3.5 19.5 - - - +
194D GLU 3.4 11.7 - - - +
195D ARG 4.8 0.9 - - - -
196D GLY* 3.8 20.2 - - - +
198D SER* 6.0 2.2 - - - +
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASN 3.5 2.2 + - - +
111B PRO* 1.3 73.0 - - - +
113B ALA* 1.3 64.0 + - - +
115B ARG* 2.9 17.0 + - - +
116B GLU* 2.9 27.6 + - - +
370B HIS* 3.1 57.5 + - + +
194D GLU* 2.8 53.4 + - + +
255D ARG* 5.5 4.1 - - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TRP* 5.1 1.3 - - + -
111B PRO* 3.2 7.6 - - + +
112B LYS* 1.3 79.3 - - - +
114B ASN* 1.3 57.1 + - - +
116B GLU* 3.8 9.9 - - - -
117B LYS* 2.7 40.2 + - + +
194D GLU 4.5 1.4 + - - +
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Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLY 3.5 3.5 + - - +
74B ILE* 3.3 35.2 - - - +
75B VAL* 3.5 32.2 + - - +
78B TRP* 3.8 10.4 - - + -
106B GLU* 4.3 6.7 - - + +
110B ASN* 2.7 27.0 + - - +
111B PRO* 3.3 11.8 + - - +
112B LYS 3.0 0.8 + - - -
113B ALA* 1.3 78.3 - - - +
115B ARG* 1.3 61.6 + - - +
118B MET* 2.9 41.8 + - + +
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Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 3.1 43.2 + - + +
107B ALA 4.2 2.2 + - - -
108B PRO* 4.9 1.8 - - - +
109B LEU 5.2 2.6 - - - +
110B ASN* 3.9 16.8 + - - +
111B PRO 3.8 2.2 + - - -
112B LYS 2.9 8.9 + - - +
114B ASN* 1.3 80.4 - - - +
116B GLU* 1.3 63.2 + - - +
118B MET* 3.2 8.4 + - - +
119B THR* 3.0 27.0 + - - +
133B VAL* 4.1 18.4 + - + +
134B ALA 6.1 1.4 - - - -
135B ILE* 3.6 24.0 - - - +
369B VAL* 3.7 26.7 - - + -
370B HIS* 3.8 27.0 - - + +
373B CYS* 5.0 0.9 - - - -
374B PHE* 3.7 30.3 + - - -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 2.9 31.6 + - - +
113B ALA* 3.8 7.3 - - - +
115B ARG* 1.3 77.8 - - - +
117B LYS* 1.3 58.2 + - - +
119B THR* 2.4 27.7 + - - -
120B GLN* 2.9 14.9 + - - +
366B PRO* 3.8 24.5 - - + +
367B SER* 4.2 16.3 - - - -
369B VAL* 4.2 4.3 - - + -
370B HIS* 3.2 35.0 + - + +
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TRP* 3.4 47.6 - - + +
113B ALA* 2.7 24.5 + - + +
116B GLU* 1.3 74.5 - - - +
118B MET* 1.3 62.4 + - - +
120B GLN* 3.1 41.5 + - - +
121B ILE* 2.9 37.5 + - - +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASN* 5.9 6.7 - - + +
75B VAL* 5.0 16.2 - - + -
78B TRP* 3.8 12.0 - - + -
81B MET* 6.1 0.4 - - + -
85B TRP* 3.8 20.7 - - + -
104B LEU* 3.3 43.1 - - + -
105B THR 4.3 9.6 - - - +
106B GLU* 4.6 18.8 - - + -
114B ASN* 2.9 30.9 + - + +
115B ARG* 3.3 6.5 - - - +
117B LYS* 1.3 74.9 - - - +
119B THR* 1.3 61.8 + - - +
121B ILE* 3.2 6.8 + - - +
122B MET* 3.0 22.7 + - - +
133B VAL* 4.2 11.4 - - + -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ARG 3.0 10.3 + - - +
116B GLU* 2.4 24.8 + - - -
118B MET* 1.3 70.4 - - - +
120B GLN* 1.3 65.9 + - - +
122B MET* 3.1 1.4 + - - +
123B PHE* 3.0 37.2 + - + -
131B MET* 3.4 35.2 - - + -
133B VAL* 4.4 3.1 - - + -
356B ILE* 4.8 6.1 - - + -
361B TYR* 5.3 0.9 - - - -
366B PRO* 3.9 9.2 + - - +
369B VAL* 3.2 37.4 - - + +
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLU 2.9 8.0 + - - +
117B LYS* 3.1 45.8 + - + +
119B THR* 1.3 81.7 + - - +
121B ILE* 1.3 57.1 + - - +
123B PHE* 4.0 0.2 - - - -
124B GLU* 2.8 52.1 + - + +
361B TYR* 4.1 16.8 - - - +
366B PRO* 4.7 16.4 - - + +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TRP* 3.4 49.4 - - + +
82B GLU* 4.8 11.0 - - + +
85B TRP* 3.6 28.5 - - + -
117B LYS* 2.9 26.9 + - - +
118B MET 3.2 7.4 + - - +
120B GLN* 1.3 74.6 - - + +
122B MET* 1.3 61.7 + - - +
125B THR* 2.7 56.7 + - + +
126B PHE* 4.6 4.5 - - + -
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 5.1 0.4 - - + -
85B TRP* 3.9 29.4 - - + +
89B PHE* 4.2 20.4 - - + -
97B PRO* 6.3 0.7 - - - -
102B VAL* 3.9 22.0 - - + -
104B LEU* 3.8 42.4 - - + -
118B MET 3.0 11.3 + - - +
119B THR 3.1 1.3 + - - +
121B ILE* 1.3 76.7 - - - +
123B PHE* 1.3 54.9 + - - +
126B PHE* 2.5 48.0 - - + +
128B THR* 3.1 15.0 - - + +
131B MET* 3.7 26.0 - - + -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR* 3.0 26.4 + - - +
122B MET* 1.3 79.5 - - - +
124B GLU* 1.3 60.9 + - - +
125B THR 3.5 1.0 + - - -
127B ASN* 3.8 25.1 - - - +
128B THR* 3.8 21.1 - - + -
130B ALA* 4.4 0.4 - - - -
131B MET* 3.5 41.3 - - + -
356B ILE* 4.0 23.6 - - + -
357B SER 4.2 1.3 - - - -
358B LYS* 3.6 37.3 - - + +
361B TYR* 3.2 59.7 - + + -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLN* 2.8 39.9 + - + +
121B ILE* 3.5 0.4 - - - -
123B PHE* 1.3 73.5 - - - +
125B THR* 1.3 63.8 + - - +
358B LYS* 6.0 1.8 - - - +
361B TYR* 3.5 31.6 + - + +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B GLU* 3.8 24.5 - - + +
121B ILE* 2.7 39.4 + - - +
123B PHE 3.4 0.2 - - - -
124B GLU* 1.3 77.8 + - - +
126B PHE* 1.3 84.8 + - + +
127B ASN* 3.5 4.1 + - - +
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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