Contacts of the helix formed by residues 129 - 145 (chain B) in PDB entry 4DAY
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 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG* 6.2 1.3 - - - +
126B SER 4.8 2.9 - - - +
127B ASP 3.7 9.0 - - - +
128B ASN* 1.3 89.7 - - - +
130B ILE* 1.3 67.8 + - + +
132B GLU* 3.8 18.1 + - + +
133B SER* 3.4 10.0 + - - -
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Residues in contact with ILE 130 (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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611A VAL* 3.7 16.4 - - + +
612A ASN* 4.1 15.0 - - + +
613A MET* 3.9 42.2 - - + +
616A LEU* 4.8 6.1 - - + -
128B ASN* 3.0 21.9 + - - +
129B PRO* 1.3 81.4 - - + +
131B HIS* 1.3 68.3 + - - +
132B GLU 3.0 3.1 - - - -
133B SER* 2.7 22.8 + - - +
134B MET* 2.8 39.2 + - + +
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LYS* 3.7 26.4 + - - -
589A CYS 3.7 23.2 + - - -
610A ASP* 4.8 2.4 + - - -
611A VAL* 3.4 24.3 - - + +
61B GLN* 3.9 1.4 + - - +
101B TYR* 3.7 17.9 + - + -
125B LEU* 3.7 38.2 - - + +
128B ASN* 3.4 39.6 + - + +
130B ILE* 1.3 78.5 - - - +
132B GLU* 1.3 56.7 - - - +
134B MET* 3.7 6.3 - - - +
135B TRP* 2.9 32.9 + - - +
138B GLU* 3.8 3.7 + - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 2.9 49.9 + - - +
75B ARG* 4.1 8.8 + - - -
77B PRO* 5.1 10.5 - - + +
101B TYR* 3.5 35.6 + - + -
128B ASN 4.6 0.6 + - - +
129B PRO* 3.8 14.9 + - + +
130B ILE 2.8 0.6 + - - -
131B HIS* 1.3 79.0 - - - +
133B SER* 1.3 66.8 + - - +
135B TRP* 3.4 11.1 + - - +
136B GLU* 4.3 2.1 + - - +
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LEU* 3.7 31.2 - - - +
129B PRO 3.4 12.1 + - - -
130B ILE* 2.7 15.9 + - - +
132B GLU* 1.3 75.8 - - - +
134B MET* 1.3 60.8 + - - -
135B TRP 3.4 0.2 + - - -
136B GLU* 3.9 11.1 + - - +
137B LEU* 4.7 4.3 - - - +
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A PRO* 4.6 0.9 - - + -
491A PHE* 4.6 10.5 - - + -
511A LYS* 4.9 3.4 - - - -
591A LEU* 6.4 0.2 - - + -
611A VAL* 4.3 22.9 - - + -
615A HIS* 3.9 14.4 - - + +
616A LEU* 3.9 39.0 - - + +
619A LEU* 3.8 29.9 - - + +
130B ILE* 2.8 40.1 + - + +
131B HIS* 3.7 2.2 - - - +
133B SER* 1.3 73.8 - - - +
135B TRP* 1.3 66.4 + - - +
137B LEU* 3.0 9.8 + - - +
138B GLU* 3.0 38.8 + - + +
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Residues in contact with TRP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 3.6 24.0 - - + -
25B VAL 3.6 17.0 - - - -
26B LEU* 3.5 21.9 - - + +
59B TRP* 3.3 45.3 - + - -
61B GLN* 3.3 39.4 - - + +
76B ASP* 3.8 9.7 + - + -
77B PRO* 4.1 15.0 - - + -
101B TYR* 3.2 18.2 - - - +
131B HIS 2.9 19.7 + - - +
132B GLU 3.7 3.8 - - - +
133B SER 3.3 1.4 - - - -
134B MET* 1.3 76.8 - - - +
136B GLU* 1.3 66.6 + - - +
137B LEU 3.2 0.3 + - - -
138B GLU* 3.3 33.7 + - + +
139B VAL* 3.4 21.3 + - + +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.7 20.6 - - + +
77B PRO* 3.9 32.6 - - + +
78B SER 5.8 0.2 - - - +
132B GLU 4.3 2.0 + - - +
133B SER 3.9 8.3 + - - +
134B MET 3.3 1.0 - - - -
135B TRP* 1.3 83.6 - - - +
137B LEU* 1.3 66.7 + - + +
139B VAL* 3.7 13.3 - - - +
140B GLU* 3.0 33.8 + - - +
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Residues in contact with LEU 137 (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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616A LEU* 3.6 34.1 - - + +
619A LEU* 4.4 17.9 - - + -
620A LYS* 4.0 26.0 - - + +
623A LEU* 4.2 13.0 - - + +
625A LYS* 4.0 24.7 - - - -
133B SER 4.7 4.9 - - - +
134B MET* 3.0 6.7 + - - +
136B GLU* 1.3 79.0 - - + +
138B GLU* 1.3 56.0 + - - +
139B VAL 2.6 17.4 + - - -
140B GLU* 2.7 27.2 + - - +
141B ASP* 3.0 12.2 + - - +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PHE* 5.0 3.8 - - + -
493A TYR* 4.0 3.6 + - - -
511A LYS* 3.0 39.9 + - + -
619A LEU* 4.2 14.2 - - + +
24B LYS* 3.2 38.4 + - - +
59B TRP* 4.4 0.2 - - - -
61B GLN* 3.9 2.3 + - - +
131B HIS* 3.8 6.9 + - - +
134B MET* 3.0 43.3 + - + +
135B TRP* 3.4 37.3 + - + +
137B LEU* 1.3 74.9 - - - +
139B VAL* 1.3 59.3 - - - +
141B ASP* 3.8 1.7 + - - -
142B LEU* 3.3 15.8 + - - +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 3.6 26.9 - - + +
26B LEU* 4.2 18.4 - - + -
29B GLN* 3.6 26.7 - - - +
135B TRP* 3.5 47.8 - - + +
136B GLU 3.7 7.9 - - - +
137B LEU 2.6 4.6 + - - -
138B GLU* 1.3 72.6 - - - +
140B GLU* 1.3 67.9 + - + +
142B LEU* 3.1 2.9 + - - +
143B HIS* 3.0 28.1 + - + -
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LEU* 3.8 21.2 - - + +
625A LYS* 3.7 19.5 + - - -
26B LEU* 6.3 1.3 - - + -
136B GLU* 3.0 32.5 - - - +
137B LEU* 2.7 21.0 + - - +
139B VAL* 1.3 75.6 - - + +
141B ASP* 1.3 56.9 + - - +
143B HIS* 2.9 10.0 + - - +
144B ARG* 2.8 32.4 + - + +
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Residues in contact with ASP 141 (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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491A PHE* 4.7 0.7 - - - -
493A TYR* 2.8 34.2 + - - +
619A LEU* 3.6 25.9 - - + +
622A ARG* 3.5 28.7 + - - +
623A LEU* 3.4 26.4 - - + +
137B LEU 3.0 13.7 + - - +
138B GLU 4.1 2.5 - - - +
140B GLU* 1.3 77.7 - - - +
142B LEU* 1.3 61.3 + - - +
144B ARG* 3.6 2.3 + - - +
145B ASN* 3.2 35.9 + - - +
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Residues in contact with LEU 142 (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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493A TYR* 3.5 23.5 + - + +
536A ASP 4.5 6.5 - - - +
537A GLY 4.5 7.6 - - - +
538A THR* 3.4 32.8 - - + -
23B LEU* 4.2 14.8 - - + -
24B LYS* 3.6 42.6 - - + +
138B GLU 3.3 11.8 + - - +
139B VAL 3.1 9.5 + - - +
141B ASP* 1.3 78.4 - - - +
143B HIS* 1.3 62.0 + - + +
145B ASN* 3.1 15.8 + - + +
146B ILE* 3.2 29.0 + - + +
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Residues in contact with HIS 143 (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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23B LEU* 3.6 22.2 - - + +
24B LYS 3.2 24.3 + - - -
25B VAL* 4.4 1.1 - - + -
29B GLN* 3.4 24.8 + - - -
139B VAL* 3.0 24.9 + - + +
140B GLU* 2.9 11.2 + - - +
142B LEU* 1.3 82.1 - - + +
144B ARG* 1.3 64.4 + - - +
146B ILE* 3.7 17.4 - - - +
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Residues in contact with ARG 144 (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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622A ARG 3.7 13.1 + - - -
623A LEU* 3.7 41.3 + - + +
624A ASN* 3.3 29.9 - - - +
140B GLU* 2.8 17.9 + - + +
141B ASP* 3.8 7.0 - - - +
143B HIS* 1.3 77.6 - - - +
145B ASN* 1.3 63.5 - - - +
146B ILE 3.4 6.2 + - - -
147B PRO* 5.1 1.2 - - - +
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Residues in contact with ASN 145 (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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483A ALA* 5.4 7.7 + - - +
485A ASP* 3.0 37.3 + - - +
493A TYR* 4.1 19.9 - - + -
495A SER* 4.9 4.9 + - - -
496A VAL* 4.3 13.2 - - + +
622A ARG* 5.0 1.7 + - - -
141B ASP* 3.2 25.3 + - - +
142B LEU* 3.1 6.0 + - - +
144B ARG* 1.3 85.5 - - - +
146B ILE* 1.3 65.2 + - + +
147B PRO* 4.0 6.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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