Contacts of the helix formed by residues 126 - 139 (chain A) in PDB entry 1D8V
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 GLY 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LEU* 1.3 83.9 - - - +
127A LEU* 1.3 70.5 + - - +
128A PRO* 3.2 5.6 - - - -
129A ALA* 2.6 19.3 + - - +
130A LEU* 3.0 4.0 + - - +
155A THR* 4.7 5.0 - - - +
169A VAL* 4.7 12.9 - - - +
172A TYR* 4.1 20.6 - - - -
175A THR 4.5 2.0 - - - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.8 19.5 - - + -
6A LEU* 3.3 17.3 - - + +
9A ALA* 3.6 34.3 - - + -
10A THR* 4.4 4.3 - - - +
14A TYR* 3.9 25.4 - - + -
126A GLY* 1.3 67.7 - - - -
128A PRO* 1.3 65.9 - - + +
130A LEU* 2.6 39.9 + - + +
155A THR* 6.1 0.4 - - - -
169A VAL* 4.2 7.0 + - - +
170A ALA* 4.9 2.7 - - - +
172A TYR 3.4 17.3 + - - +
173A VAL* 3.7 33.9 - - + +
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Residues in contact with PRO 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.6 2.9 - - + -
55A TYR* 6.0 2.9 - - + -
126A GLY 3.4 1.1 - - - -
127A LEU* 1.3 99.3 - - + +
129A ALA* 1.3 60.8 + - - +
131A SER* 2.7 33.4 + - - +
132A SER* 3.4 2.6 + - - -
172A TYR 4.0 0.7 - - - +
173A VAL 3.9 2.9 - - - +
174A ALA* 3.2 43.3 - - - +
175A THR 3.2 18.4 - - - +
176A ASN* 4.6 4.3 - - + +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 4.2 4.9 - - + +
125A LEU* 3.3 31.2 - - - +
126A GLY* 2.6 20.3 + - - +
128A PRO* 1.3 75.4 - - - +
130A LEU* 1.3 60.1 + - - +
132A SER* 2.9 22.1 + - - -
133A ALA* 3.1 9.9 + - - +
151A VAL* 4.1 12.0 - - + +
176A ASN* 3.5 22.6 - - - +
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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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4A PHE* 4.3 22.2 - - + +
6A LEU* 3.8 21.5 - - + -
52A LEU* 5.3 5.4 - - + -
126A GLY 3.0 5.3 + - - +
127A LEU* 2.6 25.9 + - + +
129A ALA* 1.3 72.4 - - - +
131A SER* 1.3 61.0 + - - +
133A ALA* 2.7 23.1 + - + +
134A ILE* 2.8 32.7 + - + +
151A VAL* 4.5 3.8 - - - +
152A LEU* 3.4 33.4 - - + -
155A THR* 3.4 22.2 - - + +
156A THR* 5.3 3.6 - - + -
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.1 28.7 - - - +
55A TYR* 4.7 14.6 - - - +
128A PRO* 2.7 18.4 + - - +
130A LEU* 1.3 77.8 - - - +
132A SER* 1.3 58.9 + - - +
134A ILE* 4.6 3.8 - - - +
135A THR* 2.4 48.7 + - - +
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO 4.0 3.5 + - - -
129A ALA* 2.9 18.6 + - - -
131A SER* 1.3 87.9 + - - +
133A ALA* 1.3 52.2 + - - +
135A THR* 4.0 5.6 - - - -
136A THR* 2.5 43.5 + - - -
148A ALA* 5.2 0.4 - - - -
151A VAL* 6.5 0.7 - - - -
176A ASN* 5.3 3.0 + - - -
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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
----------------------------------------------------------
129A ALA 3.1 6.5 + - - +
130A LEU* 2.7 34.7 + - + +
132A SER* 1.3 73.1 - - - +
134A ILE* 1.3 63.3 + - + +
136A THR* 3.8 0.3 - - - -
137A LEU* 3.0 32.8 + - + +
148A ALA* 3.5 33.2 - - - +
149A LEU* 5.3 0.2 - - - -
151A VAL* 4.3 7.8 - - + +
152A LEU* 4.3 8.3 - - + +
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Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.4 4.0 - - + -
52A LEU* 4.3 14.4 - - + +
53A THR 4.0 20.6 - - - +
54A SER* 3.5 29.8 - - - +
60A ILE* 3.7 46.3 - - + +
130A LEU* 2.8 50.7 + - + +
131A SER 4.0 1.8 - - - +
133A ALA* 1.3 73.2 - - + +
135A THR* 1.3 62.4 + - - +
137A LEU* 3.5 4.2 + - - +
138A PHE* 3.2 25.3 + - + -
152A LEU* 5.4 1.8 - - + -
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Residues in contact with THR 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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54A SER* 4.6 9.8 - - - -
55A TYR 5.6 0.2 + - - -
56A ALA* 6.1 0.9 - - - +
131A SER* 2.4 38.1 + - - -
132A SER* 3.8 4.5 - - - -
134A ILE* 1.3 75.1 - - - +
136A THR* 1.3 63.1 + - - +
138A PHE* 3.2 7.7 + - - +
139A TYR* 3.2 37.6 + - + -
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Residues in contact with THR 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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132A SER* 2.5 31.1 + - - -
135A THR* 1.3 74.9 - - - +
137A LEU* 1.3 57.7 + - - +
139A TYR* 2.7 35.6 - - - +
140A TYR* 2.8 1.0 + - - -
141A ASN* 4.5 6.3 - - + +
144A SER* 3.8 27.4 + - - +
145A ALA* 4.0 10.5 - - - +
148A ALA* 3.2 28.6 - - + +
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Residues in contact with LEU 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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60A ILE* 4.6 15.7 - - + -
74A TYR* 2.9 58.3 - - + +
76A THR* 3.8 10.9 + - - +
81A TYR* 3.5 19.8 + - + +
133A ALA* 3.0 23.0 + - + +
134A ILE* 3.8 4.3 - - - +
136A THR* 1.3 76.0 - - - +
138A PHE* 1.3 65.7 + - - +
140A TYR* 2.9 14.9 + - + +
145A ALA* 4.3 6.1 - - - +
148A ALA* 4.0 12.3 - - + -
149A LEU* 4.0 18.8 - - + -
152A LEU* 5.1 8.7 - - + -
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Residues in contact with PHE 138 (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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54A SER* 5.3 0.7 - - - -
58A GLU* 3.3 54.3 - - + +
59A THR 3.8 7.4 - - - -
60A ILE* 2.8 32.8 - - + -
76A THR* 3.2 19.6 + - + +
77A ARG* 3.5 26.5 - - + -
134A ILE* 3.2 25.2 + - + -
135A THR* 3.2 11.1 + - - +
136A THR 3.2 0.2 - - - -
137A LEU* 1.3 79.8 - - - +
139A TYR* 1.3 73.0 + - + +
140A TYR* 3.3 2.9 + - - +
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Residues in contact with TYR 139 (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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58A GLU* 5.7 3.4 - - - -
135A THR* 3.2 27.1 + - + +
136A THR* 2.7 13.0 + - - +
138A PHE* 1.3 87.5 - - + +
140A TYR* 1.3 69.2 + - - +
141A ASN* 2.7 11.6 + - - +
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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