Contacts of the helix formed by residues 114 - 127 (chain A) in PDB entry 5V5Z
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 ALA 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A VAL* 4.3 1.0 - - - +
113A SER* 1.3 71.7 - - - +
115A GLU* 1.3 67.4 + - - +
117A ALA* 3.4 3.1 + - - +
118A TYR* 3.2 29.5 + - + -
132A TYR* 4.2 7.9 - - + -
380A PHE 4.5 1.8 - - - -
381A ARG* 3.6 26.5 - - - +
468A HIS* 3.1 45.0 + - + +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 3.4 13.5 + - - +
114A ALA* 1.3 80.6 + - - +
116A ASP* 1.3 63.8 + - - +
117A ALA 2.7 16.2 + - - -
118A TYR 3.0 0.3 + - - -
119A LYS* 2.8 32.8 + - + +
132A TYR* 3.4 44.3 - - + +
134A CYS 3.9 14.7 - - - +
135A PRO* 4.1 3.5 - - - +
136A ASN* 4.1 22.2 + - - +
139A LEU* 5.7 1.6 - - - +
468A HIS* 5.0 4.2 - - - -
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 2.8 35.9 + - - +
115A GLU* 1.3 77.3 - - - +
117A ALA* 1.3 57.2 + - - +
119A LYS* 3.6 27.6 + - - +
120A HIS* 5.9 3.1 - - - -
382A LYS* 3.8 34.4 + - + +
384A THR* 4.3 9.9 - - - +
401A TYR* 3.9 6.9 + - - -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 6.0 0.2 + - - -
113A SER 4.0 0.8 + - - -
114A ALA 3.4 8.7 + - - +
115A GLU 2.7 4.9 + - - -
116A ASP* 1.3 76.7 - - - +
118A TYR* 1.3 65.6 + - + +
119A LYS 3.4 2.5 + - - -
120A HIS* 5.1 2.3 + - - +
233A PHE* 3.8 21.0 - - - -
380A PHE* 3.6 38.4 - - + -
381A ARG 4.2 7.6 - - - -
401A TYR* 4.1 17.2 - - + -
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Residues in contact with TYR 118 (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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114A ALA* 3.2 16.5 + - + +
115A GLU 3.0 2.4 + - - -
117A ALA* 1.3 79.2 - - + +
119A LYS* 1.3 63.4 + - - +
120A HIS 3.7 0.9 - - - -
121A LEU* 3.6 4.1 + - + +
122A THR* 3.1 27.4 + - + +
132A TYR* 3.5 39.0 - + + -
233A PHE* 4.4 11.7 - + - -
379A ILE* 3.5 6.2 - - - +
380A PHE* 3.0 46.1 + + + -
381A ARG* 3.7 7.4 - - - -
601A HEM 2.6 29.2 + - - -
602A 1YN 3.3 52.4 - + - -
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Residues in contact with LYS 119 (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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115A GLU* 2.8 18.3 + - + +
116A ASP* 3.6 26.0 + - - +
117A ALA 3.4 2.8 - - - -
118A TYR* 1.3 73.5 - - - +
120A HIS* 1.3 81.3 + - + +
121A LEU 2.8 10.9 + - - -
122A THR* 4.5 0.2 - - - -
123A THR* 3.0 43.3 + - + +
132A TYR* 3.9 26.2 - - - +
133A ASP* 4.4 11.7 - - - +
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Residues in contact with HIS 120 (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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116A ASP 5.9 3.8 - - - -
117A ALA 5.1 1.9 + - - +
119A LYS* 1.3 97.3 - - + +
121A LEU* 1.3 58.1 + - - +
124A PRO* 3.5 12.9 - - - +
232A ASN* 3.5 17.6 - - - +
233A PHE* 4.8 13.7 - - + +
236A PRO* 3.1 38.0 - - + +
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Residues in contact with LEU 121 (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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118A TYR* 3.6 3.6 + - + +
119A LYS 2.8 3.0 + - - -
120A HIS* 1.3 80.1 - - - +
122A THR* 1.3 82.8 + - + +
124A PRO* 3.3 7.4 - - - +
125A VAL* 3.3 17.5 - - - +
228A PHE* 3.2 35.0 - - + -
229A THR 3.7 3.1 - - - +
230A PRO 4.7 0.2 - - - -
232A ASN* 3.2 37.6 + - + +
233A PHE* 3.2 32.2 - - + -
508A MET* 3.4 37.9 - - + -
602A 1YN 5.3 3.8 - - + +
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Residues in contact with THR 122 (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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118A TYR* 3.1 18.8 + - + +
119A LYS 3.9 0.9 + - - -
121A LEU* 1.3 93.6 - - + +
123A THR* 1.3 64.3 + - - +
125A VAL* 2.9 7.9 + - - +
126A PHE* 2.8 58.7 + - + -
131A ILE* 4.7 0.9 - - - +
132A TYR* 3.6 25.8 + - + +
228A PHE* 4.7 1.1 - - + -
602A 1YN 4.0 25.4 - - - +
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Residues in contact with THR 123 (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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119A LYS* 3.0 25.1 + - + +
122A THR* 1.3 82.2 + - - +
124A PRO* 1.3 63.9 - - + +
125A VAL 2.8 1.6 + - - -
126A PHE* 5.1 0.7 - - - -
127A GLY* 2.7 36.7 + - - +
128A LYS* 4.6 20.4 - - + -
130A VAL 4.8 1.3 + - - -
132A TYR 4.3 0.2 - - - -
133A ASP* 3.2 44.2 + - + +
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Residues in contact with PRO 124 (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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119A LYS 3.6 2.7 - - - +
120A HIS* 3.5 21.5 - - - +
121A LEU 3.3 13.2 - - - +
123A THR* 1.3 97.7 - - + +
125A VAL* 1.3 58.1 + - + +
127A GLY* 4.6 0.9 - - - -
236A PRO* 4.4 2.0 - - + -
237A ASN* 3.8 19.1 - - - +
246A ARG* 3.5 44.4 + - - +
247A ASP* 4.2 6.0 - - - +
250A GLN* 4.5 9.4 - - - +
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Residues in contact with VAL 125 (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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121A LEU 3.3 18.8 - - - +
122A THR 2.9 6.8 + - - +
124A PRO* 1.3 82.4 - - + +
126A PHE* 1.3 71.7 + - + +
224A LEU* 3.3 30.5 - - + +
227A GLY 3.6 23.3 - - - +
228A PHE* 3.8 26.7 - - + -
232A ASN* 4.4 0.2 - - - +
246A ARG* 4.1 5.4 - - - +
250A GLN* 3.6 7.8 - - - +
302A ILE* 3.9 4.7 - - - +
306A MET* 3.8 28.7 - - - -
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Residues in contact with PHE 126 (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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122A THR* 2.8 38.8 + - + +
123A THR* 5.1 0.4 - - - -
125A VAL* 1.3 97.1 - - + +
127A GLY* 1.3 62.9 + - - +
131A ILE* 3.4 23.6 - - + -
228A PHE* 4.3 11.9 - + - -
250A GLN* 3.7 10.6 - - - +
299A ASN* 3.0 31.6 - - - +
302A ILE* 3.5 12.0 - - + +
303A GLY* 3.4 36.6 - - - +
306A MET* 3.7 21.5 - - + -
602A 1YN 3.8 30.5 - + + -
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Residues in contact with GLY 127 (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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123A THR* 2.7 30.4 + - - +
124A PRO 5.4 0.2 - - - -
125A VAL 3.7 0.6 - - - -
126A PHE* 1.3 78.9 - - - +
128A LYS* 1.3 67.6 + - - +
130A VAL* 4.0 14.6 + - - +
250A GLN* 4.1 13.6 - - - +
299A ASN* 3.1 12.0 + - - -
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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