Contacts of the helix formed by residues 127 - 137 (chain A) in PDB entry 5NDD
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 TRP 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.2 30.7 + - - +
124A SER* 3.3 9.5 + - - +
125A VAL 3.1 0.8 - - - -
126A ILE* 1.3 88.6 - - + +
128A PHE* 1.3 65.3 + - + +
129A PRO* 3.4 1.3 - - - -
130A LEU* 3.2 27.2 + - + +
131A LYS* 3.1 17.2 + - - +
147A LEU* 3.9 24.9 - - + -
150A VAL* 3.8 14.8 - - + -
151A LEU* 3.7 36.6 - - + +
154A PHE* 3.8 24.4 - + + -
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Residues in contact with PHE 128 (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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82A TYR* 3.4 40.6 - + + -
85A VAL* 3.7 26.9 - - + -
86A PHE* 4.1 13.0 - - + -
124A SER* 3.2 34.5 - - - -
125A VAL* 3.0 22.6 + - + +
127A TRP* 1.3 76.4 - - + +
129A PRO* 1.4 59.6 - - + +
131A LYS* 2.8 39.4 + - + -
132A ILE* 2.5 42.4 + - + +
155A PHE* 6.0 0.2 - + - -
334A THR* 4.0 16.8 - - + -
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Residues in contact with PRO 129 (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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86A PHE* 3.7 32.8 - - + -
126A ILE 3.2 17.0 - - - +
127A TRP 3.5 0.9 - - - -
128A PHE* 1.4 91.9 - - + +
130A LEU* 1.3 64.9 + - + +
132A ILE* 4.1 10.0 - - + +
133A ALA* 3.2 26.7 + - - +
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Residues in contact with LEU 130 (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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126A ILE 5.1 2.5 - - - +
127A TRP* 3.2 32.9 + - + +
128A PHE 3.1 0.4 - - - -
129A PRO* 1.3 88.4 - - + +
131A LYS* 1.3 64.3 + - - +
133A ALA* 4.0 3.6 - - + +
134A TYR* 3.1 23.9 + - - +
141A TRP* 3.7 25.0 - - + -
143A TYR* 3.6 41.3 - - + +
147A LEU* 5.3 7.9 - - + -
151A LEU* 4.6 3.4 - - + -
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Residues in contact with LYS 131 (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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82A TYR* 3.5 25.4 + - + -
127A TRP 3.1 6.7 + - - +
128A PHE* 2.8 50.1 + - + +
130A LEU* 1.3 77.2 - - - +
132A ILE* 1.3 63.4 + - + +
134A TYR* 3.3 11.2 - - - +
135A HIS* 3.1 24.6 - - + +
141A TRP* 5.0 0.2 - - - -
151A LEU* 4.2 12.5 - - + +
155A PHE* 3.9 19.8 - - - +
334A THR* 3.8 20.8 - - - +
2201A 8TZ 3.1 46.2 - - + +
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Residues in contact with ILE 132 (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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79A PRO* 3.7 16.3 - - + +
82A TYR* 3.9 24.2 - - + +
83A THR* 3.3 43.3 - - + +
86A PHE* 4.6 8.5 - - + -
128A PHE* 2.5 31.1 + - + +
129A PRO* 4.1 8.1 - - + +
131A LYS* 1.3 72.0 - - - +
133A ALA* 1.3 64.7 + - - +
135A HIS* 3.2 5.9 + - - +
136A ILE* 3.1 46.5 + - + +
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Residues in contact with ALA 133 (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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129A PRO 3.2 17.9 + - - +
130A LEU* 4.0 5.8 - - + +
131A LYS 3.4 0.2 - - - -
132A ILE* 1.3 78.3 - - - +
134A TYR* 1.3 63.4 + - - +
136A ILE* 3.5 8.6 + - - +
137A HIS* 3.0 42.5 + - + +
143A TYR* 4.0 18.8 - - - +
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Residues in contact with TYR 134 (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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130A LEU 3.1 19.8 + - - +
131A LYS* 3.3 5.6 - - - +
133A ALA* 1.3 79.2 - - - +
135A HIS* 1.3 87.0 + + - +
137A HIS* 3.6 4.0 + - - -
139A ASN* 3.1 44.1 + - - +
140A ASN 3.2 33.1 + - - +
141A TRP* 3.6 30.3 - + + -
143A TYR* 5.4 3.1 - - - -
225A THR* 3.4 8.8 - - - -
226A CYS* 2.8 31.0 + - + -
228A ASP* 2.6 29.3 + - - -
2201A 8TZ 3.6 20.6 - - + -
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Residues in contact with HIS 135 (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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74A THR* 3.2 21.6 + - + +
75A THR* 3.4 20.9 - - - +
78A LEU* 3.5 19.6 - - + +
79A PRO* 4.0 9.4 - - + -
82A TYR* 3.7 20.7 - + - -
131A LYS 3.1 23.8 + - - -
132A ILE* 3.2 5.4 + - - +
134A TYR* 1.3 93.2 - + - +
136A ILE* 1.3 68.0 + - - +
137A HIS 3.1 1.6 - - - -
138A GLY 3.0 10.9 + - - -
139A ASN* 2.9 23.1 + - - -
228A ASP* 4.3 4.0 - - - -
2201A 8TZ 2.6 35.2 + + - -
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Residues in contact with ILE 136 (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 THR* 4.0 14.9 + - - +
79A PRO* 3.6 18.4 - - + -
132A ILE* 3.1 35.8 + - + +
133A ALA* 3.9 8.5 - - - +
135A HIS* 1.3 76.9 - - - +
137A HIS* 1.3 73.5 + - + +
138A GLY 3.3 3.5 + - - -
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Residues in contact with HIS 137 (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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133A ALA* 3.0 35.3 + - + +
134A TYR 3.9 2.5 - - - +
135A HIS 3.1 1.4 - - - -
136A ILE* 1.3 90.2 + - + +
138A GLY* 1.3 61.8 + - - +
139A ASN 3.5 2.2 - - - -
140A ASN* 3.5 25.4 - - + +
142A ILE* 6.3 2.9 - - + -
143A TYR* 5.6 3.1 - - - -
223A ILE* 4.9 1.9 - - - +
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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