Contacts of the strand formed by residues 106 - 113 (chain t) in PDB entry 5GJQ
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 VAL 106 (chain t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54t CYS* 4.1 11.7 - - + -
55t SER 3.6 5.4 - - - +
60t ASP* 3.7 36.1 - - + +
61t CYS* 3.9 8.7 - - - +
64t LEU* 3.8 11.7 - - + -
96t LEU* 5.1 1.6 - - + +
104t TYR* 2.9 16.9 + - + +
105t TYR* 1.3 82.2 - - - +
107t TYR* 1.3 69.7 + - - +
108t ASN* 3.2 39.9 + - - +
125t ASP 4.3 2.4 - - - -
126t PRO* 3.7 23.3 - - - +
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Residues in contact with TYR 107 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7t PHE* 5.7 5.8 - + - -
12t ILE* 4.9 1.4 - - - +
53t GLY 3.7 0.7 - - - +
54t CYS* 3.5 2.1 - - - -
55t SER* 2.9 47.5 + - - +
56t GLY* 5.0 4.5 - - - -
105t TYR* 4.0 28.6 + + - -
106t VAL* 1.3 71.8 - - - +
108t ASN* 1.3 61.3 + - - +
109t ILE* 5.3 2.3 - - + +
124t PHE 4.0 16.6 - - - +
125t ASP* 4.8 1.8 - - + -
126t PRO* 3.7 30.3 - - + +
138t GLY* 5.0 7.0 - - - -
139t GLY* 4.6 24.5 - - - +
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Residues in contact with ASN 108 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52t ILE* 3.4 10.6 - - + +
53t GLY 3.2 4.9 - - - +
54t CYS* 3.0 29.6 - - - -
64t LEU* 3.6 15.9 - - - +
92t LEU* 3.9 28.0 - - + +
96t LEU* 4.1 11.5 - - - +
106t VAL* 3.2 31.3 + - - +
107t TYR* 1.3 71.4 - - - +
109t ILE* 1.3 68.8 + - - +
110t ILE 4.2 0.2 - - - -
124t PHE* 3.1 36.0 + - + +
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Residues in contact with ILE 109 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12t ILE* 3.8 23.8 - - + -
13t LEU 4.8 0.2 - - - +
14t ALA* 3.7 25.6 - - + -
23t VAL* 4.6 3.6 - - + +
51t VAL 4.0 0.2 - - - +
52t ILE* 3.6 1.0 - - - -
53t GLY 2.9 33.6 + - - -
107t TYR* 5.3 2.7 - - + +
108t ASN* 1.3 80.9 - - - +
110t ILE* 1.3 63.1 + - - +
111t GLY 3.9 0.3 + - - -
121t VAL* 3.9 14.1 - - + -
122t TYR 3.3 11.4 - - - +
123t SER* 4.7 4.9 - - - -
136t LYS* 3.4 33.0 - - + +
137t ALA 3.9 1.1 - - - -
138t GLY* 3.6 26.5 - - - +
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Residues in contact with ILE 110 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46t LEU* 5.1 0.2 - - + -
50t THR* 3.8 14.4 - - + -
51t VAL 3.6 3.6 - - - +
52t ILE* 3.9 24.0 - - + -
85t THR* 3.6 30.1 - - + +
88t ILE* 3.6 27.6 - - + -
89t ALA* 3.7 23.3 - - + -
92t LEU* 4.1 7.6 - - + -
108t ASN 4.2 0.2 - - - -
109t ILE* 1.3 74.7 - - - +
111t GLY* 1.3 60.4 + - - +
121t VAL* 3.3 6.1 - - - +
122t TYR* 2.8 41.1 + - + +
124t PHE* 3.8 16.8 - - + -
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Residues in contact with GLY 111 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21t ALA* 4.3 5.6 - - - -
23t VAL* 3.7 18.8 - - - +
50t THR* 3.7 0.7 - - - +
51t VAL* 2.8 37.3 + - - +
109t ILE 3.9 1.2 + - - -
110t ILE* 1.3 77.7 - - - +
112t GLY* 1.3 59.4 + - - -
120t ALA 3.4 7.2 - - - -
121t VAL* 4.0 9.6 - - - -
198t VAL* 4.7 1.3 - - - +
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Residues in contact with GLY 112 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21t ALA* 3.4 18.1 - - - +
49t LYS 3.1 14.1 - - - -
50t THR* 4.3 0.4 - - - -
85t THR* 4.0 9.8 - - - +
111t GLY* 1.3 73.8 - - - -
113t LEU* 1.3 64.3 + - - -
119t GLY* 3.5 2.1 - - - -
120t ALA* 2.8 33.9 + - - -
198t VAL* 4.1 3.4 - - - -
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Residues in contact with LEU 113 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19t ASP 4.2 9.4 - - - +
20t PHE* 4.2 4.9 - - - -
49t LYS* 3.0 36.5 + - + +
85t THR* 2.9 21.5 + - - -
112t GLY* 1.3 81.7 - - - +
114t ASP* 1.3 69.0 + - - +
115t GLU* 4.9 0.2 - - - +
117t GLY* 3.5 27.1 - - - +
118t LYS 3.3 9.6 - - - +
119t GLY* 4.1 3.1 - - - +
120t ALA* 4.9 0.9 - - - -
198t VAL* 3.7 25.8 - - + +
199t THR 3.6 31.9 - - - +
200t LYS* 3.9 7.6 - - + +
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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