Contacts of the helix formed by residues 111 - 125 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A THR* 3.5 17.5 - - - +
194A GLU 3.4 13.0 - - - +
195A ARG 4.8 1.1 - - - -
196A GLY* 3.8 19.5 - - - -
198A SER* 6.1 0.9 - - - +
74D ILE* 3.5 25.6 - - + -
106D GLU* 4.1 3.3 - - - +
109D LEU 3.9 2.9 - - - +
110D ASN* 1.3 101.4 - - - +
112D LYS* 1.3 66.1 + - - +
113D ALA* 3.2 9.6 - - + +
114D ASN* 3.3 18.5 + - - +
115D ARG* 3.8 3.6 + - - -
176D ARG* 3.9 5.2 - - - +
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLU* 2.9 52.0 + - + +
255A ARG* 5.6 3.5 - - - +
110D ASN 3.5 1.5 + - - +
111D PRO* 1.3 71.5 - - - +
113D ALA* 1.3 64.7 + - - +
115D ARG* 2.9 16.8 + - - +
116D GLU* 2.9 27.6 + - - +
370D HIS* 3.1 54.9 + - + +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLU 4.7 0.8 + - - -
78D TRP* 5.1 1.1 - - + -
111D PRO* 4.9 6.3 - - + -
112D LYS* 1.3 78.2 - - - +
114D ASN* 1.3 56.8 + - - +
116D GLU* 3.8 11.4 - - - +
117D LYS* 2.6 40.9 + - + +
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Residues in contact with ASN 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D GLY 3.5 3.7 + - - +
74D ILE* 3.3 34.9 - - - +
75D VAL* 3.5 31.9 + - - +
78D TRP* 3.8 9.7 - - + -
106D GLU* 4.3 6.5 - - + +
110D ASN* 2.7 27.2 + - - +
111D PRO* 3.3 11.7 + - - +
112D LYS 3.0 0.8 - - - -
113D ALA* 1.3 78.6 - - - +
115D ARG* 1.3 61.2 + - - +
118D MET* 2.9 40.2 + - + +
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLU* 3.1 42.2 + - + +
107D ALA 4.1 2.2 + - - -
108D PRO* 4.9 1.6 - - - +
109D LEU 5.1 2.2 - - - +
110D ASN* 4.0 17.6 + - - +
111D PRO 3.8 2.2 + - - -
112D LYS 2.9 8.4 + - - +
114D ASN* 1.3 79.6 - - - +
116D GLU* 1.3 64.0 + - - +
118D MET* 3.2 9.0 + - - +
119D THR* 3.0 27.2 + - - +
133D VAL* 4.1 18.9 + - + +
134D ALA 6.1 1.6 - - - -
135D ILE* 3.6 24.0 - - - +
369D VAL* 3.7 26.7 - - + -
370D HIS* 3.8 27.1 + - + +
373D CYS* 5.0 0.9 - - - -
374D PHE* 3.7 28.9 + - - -
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 2.9 31.5 + - - +
113D ALA* 3.8 7.5 - - - +
115D ARG* 1.3 76.6 - - - +
117D LYS* 1.3 58.2 + - - +
119D THR* 2.4 28.3 + - - -
120D GLN* 2.9 13.8 + - - +
366D PRO* 3.8 25.4 - - + +
367D SER* 4.2 16.0 - - - +
369D VAL* 4.2 4.7 - - + -
370D HIS* 3.2 35.3 + - + +
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Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D TRP* 3.4 46.7 - - + +
113D ALA* 2.6 25.2 + - + +
116D GLU* 1.3 74.7 - - - +
118D MET* 1.3 60.7 + - - +
120D GLN* 3.1 40.6 + - - +
121D ILE* 2.9 39.3 + - - +
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Residues in contact with MET 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 5.9 7.2 - - + +
75D VAL* 5.0 16.4 - - + -
78D TRP* 3.8 12.4 - - + -
81D MET* 6.4 0.4 - - - -
85D TRP* 3.8 21.2 - - + -
104D LEU* 3.4 42.6 - - + -
105D THR 4.2 9.6 - - - +
106D GLU* 4.6 18.6 - - + -
114D ASN* 2.9 29.9 + - + +
115D ARG* 3.3 6.7 - - - +
117D LYS* 1.3 74.3 - - - +
119D THR* 1.3 62.0 + - - +
121D ILE* 3.2 6.2 + - - +
122D MET* 3.0 23.1 + - - +
133D VAL* 4.2 12.6 - - + -
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ARG 3.0 10.3 + - - +
116D GLU* 2.4 23.9 + - - -
118D MET* 1.3 71.1 - - - +
120D GLN* 1.3 64.9 + - - +
122D MET* 3.1 1.9 + - - -
123D PHE* 3.0 38.1 + - + -
131D MET* 3.4 35.0 - - + -
133D VAL* 4.5 3.4 - - + -
356D ILE* 4.8 6.3 - - + -
361D TYR* 5.3 0.9 - - - -
366D PRO* 3.9 9.3 + - - +
369D VAL* 3.2 37.0 - - + +
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Residues in contact with GLN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU 2.9 7.8 + - - +
117D LYS* 3.1 42.5 + - + +
119D THR* 1.3 82.5 + - - +
121D ILE* 1.3 57.1 + - + +
123D PHE* 4.0 0.3 - - - +
124D GLU* 2.8 50.6 + - + +
361D TYR* 4.1 16.2 - - - +
366D PRO* 4.7 16.1 - - + +
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D TRP* 3.4 49.4 - - + +
82D GLU* 4.8 9.9 - - + -
85D TRP* 3.6 28.3 - - + -
117D LYS* 2.9 27.3 + - - +
118D MET 3.5 7.4 - - - +
120D GLN* 1.3 73.8 - - - +
122D MET* 1.3 63.2 + - - +
124D GLU 4.9 0.2 - - - -
125D THR* 2.7 55.5 + - + +
126D PHE* 4.6 4.0 - - + -
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Residues in contact with MET 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D TRP* 3.9 31.0 - - + -
89D PHE* 4.2 21.1 - - + -
97D PRO* 6.3 0.4 - - - -
102D VAL* 3.8 21.5 - - + -
104D LEU* 3.8 40.8 - - + -
118D MET 3.0 11.7 + - - +
119D THR 3.1 1.1 + - - +
121D ILE* 1.3 77.5 - - - +
123D PHE* 1.3 54.1 + - - +
126D PHE* 2.5 48.1 - - + +
128D THR* 3.0 16.3 - - + +
131D MET* 3.7 25.6 - - + -
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Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D THR* 3.0 26.8 + - - +
122D MET* 1.3 79.6 - - - +
124D GLU* 1.3 59.6 + - - +
125D THR 3.4 2.9 + - - -
127D ASN* 3.8 26.0 - - - +
128D THR* 3.9 20.4 - - + +
130D ALA* 4.4 3.4 - - - -
131D MET* 3.6 35.7 - - + -
356D ILE* 4.0 25.4 - - + -
357D SER 4.2 0.9 - - - -
358D LYS* 3.6 37.4 - - + +
361D TYR* 3.2 59.9 - + + -
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLN* 2.8 39.8 + - + +
121D ILE 3.5 0.4 - - - -
123D PHE* 1.3 74.0 - - - +
125D THR* 1.3 63.9 + - - +
358D LYS* 6.0 1.8 - - - +
361D TYR* 3.5 31.8 + - + +
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Residues in contact with THR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 3.8 24.3 - - + +
121D ILE* 2.7 39.7 + - - +
124D GLU* 1.3 77.8 + - - +
126D PHE* 1.3 85.1 + - + +
127D ASN 3.5 3.3 + - - -
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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