Contacts of the helix formed by residues 116 - 129 (chain A) in PDB entry 4GDY
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 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 2.6 34.1 + - - -
115A SER* 1.3 74.6 - - - +
117A SER* 1.4 60.6 + - - -
118A GLN 3.2 3.1 + - - -
119A GLN 3.6 2.4 + - - -
262A SER* 5.5 0.2 - - - -
270A ARG* 3.3 28.1 + - - -
271A ILE 4.0 6.5 - - - -
272A GLY* 3.9 11.2 - - - -
501A 0X1 3.7 2.2 - - - -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 4.2 4.9 - - - -
116A GLY* 1.4 69.6 - - - -
118A GLN* 1.3 63.0 + - - +
119A GLN 3.3 0.2 - - - -
120A GLY* 3.4 3.2 + - - -
121A LEU* 3.2 26.3 + - - +
230A ASP* 4.3 5.0 + - - -
232A PRO* 5.2 0.9 - - - +
258A ALA* 4.4 16.7 - - - +
259A ASP 3.5 25.1 - - - -
260A SER* 3.7 9.4 - - - -
272A GLY* 4.1 2.8 - - - -
273A PHE 5.1 1.1 - - - +
274A LEU* 5.0 1.1 - - - +
501A 0X1 2.7 43.0 + - - -
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 1.3 75.8 + - - +
119A GLN* 1.3 58.7 + - - +
121A LEU* 3.6 16.6 + - - +
122A CYS* 3.0 30.9 + - - +
125A PHE* 5.5 1.2 - - - -
142A TYR* 3.3 35.4 + - - -
144A GLY* 4.1 9.8 + - - -
145A THR* 5.4 1.6 - - - +
148A SER* 3.7 15.4 + - - -
270A ARG* 4.2 6.7 - - - +
501A 0X1 3.0 25.3 + - - +
289B GLN 4.6 0.7 - - - +
290B VAL* 3.4 24.8 + - - +
291B SER 3.1 16.2 - - - +
293B LEU* 4.2 15.5 - - + -
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Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.7 8.2 - - - -
115A SER* 2.8 46.3 + - - +
116A GLY 3.6 2.5 + - - +
117A SER 3.3 0.8 - - - -
118A GLN* 1.3 73.6 - - - +
120A GLY* 1.3 65.4 + - - +
122A CYS* 3.4 3.3 + - - +
123A LYS* 3.0 44.8 + - + +
288A ILE* 4.0 21.9 - - - +
291A SER* 4.7 7.9 - - - -
292A THR* 3.0 37.9 + - - +
295A PRO* 5.9 0.3 - - - +
119B GLN* 5.4 0.2 - - - +
291B SER* 2.9 18.2 + - - +
292B THR* 3.9 14.4 - - + +
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Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.9 19.6 - - - -
117A SER 3.4 6.5 + - - -
119A GLN* 1.3 79.8 - - - +
121A LEU* 1.4 60.3 + - - +
123A LYS* 3.4 4.6 + - - +
124A VAL* 3.0 28.6 + - - +
274A LEU* 3.7 28.7 - - - +
284A VAL* 4.9 0.7 - - - -
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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
----------------------------------------------------------
117A SER* 3.2 23.8 + - - +
118A GLN* 3.7 15.5 - - - +
120A GLY* 1.4 72.2 - - - +
122A CYS* 1.3 56.2 + - - +
124A VAL* 3.3 7.6 + - - +
125A PHE* 2.9 51.1 + - + -
142A TYR* 5.5 1.1 - - + -
145A THR* 5.6 2.7 - - + -
195A TYR* 4.0 9.4 - - + +
228A ILE* 4.0 26.2 - - + -
230A ASP* 3.5 42.2 - - + +
258A ALA* 4.3 11.9 - - + -
274A LEU* 4.3 2.5 - - + +
501A 0X1 3.9 16.6 - - + -
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Residues in contact with CYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.0 20.3 + - - +
119A GLN 3.5 4.9 - - - +
120A GLY 3.3 0.2 - - - -
121A LEU* 1.3 75.3 - - - +
123A LYS* 1.4 69.0 + - - +
125A PHE* 3.3 11.2 + - - +
126A GLU* 3.0 57.4 + - - +
148A SER* 4.9 4.0 - - - +
287B HIS* 4.8 1.8 - - - -
290B VAL* 3.3 25.6 - - - +
291B SER* 3.9 19.3 - - - -
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.0 36.7 + - + +
120A GLY 3.9 3.4 - - - +
122A CYS* 1.4 93.4 - - - +
124A VAL* 1.4 57.3 + - - +
126A GLU* 3.6 8.8 + - - +
127A MET* 3.1 28.6 + - - +
284A VAL* 4.0 25.2 - - + +
287A HIS* 3.4 45.5 + - + +
288A ILE* 4.1 21.1 - - + -
291A SER* 3.7 17.3 + - - +
123B LYS* 3.3 27.5 - - - +
291B SER* 4.8 2.7 - - - -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY 3.0 22.0 + - - +
121A LEU* 3.5 6.7 - - - +
123A LYS* 1.4 72.7 - - - +
125A PHE* 1.3 66.2 + - + +
127A MET* 3.3 9.0 + - + +
128A ILE* 3.3 42.3 + - + +
228A ILE* 3.8 22.9 - - + -
256A ILE* 4.0 28.3 - - + -
274A LEU* 3.6 24.2 - - + -
284A VAL* 3.7 12.6 - - + -
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 5.5 1.3 - - - -
121A LEU* 2.9 39.5 + - + +
122A CYS* 3.3 6.0 + - - +
124A VAL* 1.3 75.5 - - + +
126A GLU* 1.4 57.1 + - + +
128A ILE* 4.0 2.2 - - - -
129A ILE* 3.0 41.6 + - + +
145A THR* 4.0 25.6 - - - -
148A SER* 4.0 20.6 - - - -
149A LEU* 3.6 22.2 - - + -
152A LEU* 4.0 17.2 - - + +
193A PHE* 3.9 25.8 - + - -
195A TYR* 4.0 25.4 - + - -
228A ILE* 4.0 19.7 - - + -
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Residues in contact with GLU 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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8A THR* 3.9 13.5 + - - +
122A CYS* 3.0 33.1 + - - +
123A LYS* 3.8 13.6 + - - +
124A VAL 3.3 0.2 - - - -
125A PHE* 1.4 73.1 - - + +
127A MET* 1.3 62.8 + - - +
128A ILE 3.4 0.2 - - - -
129A ILE 4.3 5.4 - - - +
152A LEU* 4.3 23.9 - - + +
287A HIS* 3.2 31.7 + - + -
14B ARG* 4.7 4.9 + - - -
126B GLU* 4.3 6.5 - - - +
287B HIS* 3.2 26.0 + - - -
290B VAL* 5.6 0.7 - - - +
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Residues in contact with MET 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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6A PHE 3.5 6.9 - - - +
7A ILE* 4.4 4.0 - - - -
8A THR* 2.8 38.8 + - - +
11A SER* 3.5 22.4 - - - +
123A LYS 3.1 17.8 + - - +
124A VAL* 3.3 11.8 + - + +
126A GLU* 1.3 75.3 - - - +
128A ILE* 1.3 83.5 + - + +
226A LEU* 5.5 0.2 - - + -
256A ILE* 4.4 10.3 - - + -
280A LEU* 3.7 54.7 - - + +
283A ARG* 3.7 14.1 - - + -
284A VAL* 4.4 6.3 - - + -
287A HIS* 5.8 0.2 + - - -
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Residues in contact with ILE 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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6A PHE* 3.4 26.8 - - + +
8A THR* 3.5 10.0 + - - +
124A VAL* 3.3 37.3 + - + +
125A PHE 4.1 1.6 - - - +
127A MET* 1.3 89.5 - - + +
129A ILE* 1.4 65.1 + - + +
192A LYS* 2.9 59.8 + - + +
193A PHE* 3.9 26.9 - - + -
226A LEU* 4.4 14.8 - - + -
228A ILE* 4.2 4.3 - - + -
256A ILE* 4.7 0.9 - - + -
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Residues in contact with ILE 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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8A THR* 3.9 8.2 - - - +
125A PHE* 3.0 27.1 + - + +
126A GLU 4.3 6.2 - - - +
127A MET 4.0 0.4 - - - -
128A ILE* 1.4 72.5 - - + +
130A ASN* 1.3 72.4 + - - +
131A PRO* 4.8 1.4 - - - +
133A ASP* 3.8 6.7 - - + -
135A VAL* 4.2 11.2 - - + -
149A LEU* 3.7 30.1 - - + -
152A LEU* 3.6 37.5 - - + +
154A CYS* 3.6 25.8 - - + -
192A LYS* 6.0 0.2 - - + -
193A PHE* 3.8 26.0 - - + -
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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