Contacts of the strand formed by residues 115 - 124 (chain A) in PDB entry 4JDA
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 THR 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLU* 3.2 30.5 + - - +
105A VAL 3.1 9.4 + - - +
106A SER* 4.5 4.7 - - - -
107A VAL* 3.6 6.6 - - - +
114A SER* 1.3 91.8 + - - +
116A SER* 1.3 60.3 + - - +
117A VAL* 4.8 1.8 - - + +
137A GLY* 3.8 16.8 - - - -
138A GLU* 3.1 22.0 + - + +
139A HIS* 2.6 29.3 + - - -
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG 3.8 0.7 - - - +
104A GLU* 3.3 1.1 - - - -
105A VAL* 2.5 56.6 + - - +
107A VAL* 5.6 0.4 - - - -
115A THR* 1.3 80.0 - - - +
117A VAL* 1.3 64.0 + - - +
118A GLU* 4.1 3.4 + - - +
134A VAL* 3.6 16.8 - - - +
136A GLY 3.6 6.7 + - - -
139A HIS* 3.3 20.0 - - - -
301A A9S 3.7 18.9 - - - +
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Residues in contact with VAL 117 (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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88A ARG* 6.0 1.6 - - + -
102A ILE* 3.7 23.8 - - + -
103A ARG 3.3 6.5 - - - +
104A GLU* 4.6 13.0 - - + +
115A THR* 5.2 3.8 - - + -
116A SER* 1.3 73.9 - - - +
118A GLU* 1.3 56.1 + - - +
134A VAL* 3.6 2.8 - - - -
135A LEU* 2.7 45.9 + - + -
136A GLY* 3.0 33.9 + - - +
137A GLY* 3.7 5.4 - - - +
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Residues in contact with GLU 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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72A PHE* 3.9 3.7 - - + -
101A THR 3.8 0.5 - - - +
102A ILE* 3.3 7.2 - - - +
103A ARG* 2.9 52.6 + - + +
105A VAL* 6.4 0.9 - - + -
116A SER* 4.1 4.9 - - - +
117A VAL* 1.3 74.9 - - - +
119A ILE* 1.3 59.9 + - - +
132A PHE* 3.6 32.3 - - + -
133A ARG 3.2 5.6 - - - +
134A VAL* 4.6 4.0 - - + -
135A LEU* 4.6 0.4 - - - -
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Residues in contact with ILE 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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72A PHE* 4.3 0.2 - - - -
100A GLY* 3.4 38.4 - - - +
101A THR 3.4 3.1 - - - +
102A ILE* 3.6 16.8 - - + -
118A GLU* 1.3 72.6 - - - +
120A LEU* 1.3 65.0 + - - +
121A GLU* 3.5 20.6 + - + +
132A PHE* 3.2 5.3 - - - -
133A ARG* 2.7 43.6 + - + +
135A LEU* 3.5 35.1 - - + +
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Residues in contact with LEU 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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72A PHE* 3.6 32.4 - - + -
97A ILE* 3.5 31.6 - - + -
98A LYS 3.8 17.7 - - - +
99A VAL* 3.6 6.4 - - - +
100A GLY* 2.7 31.5 + - - -
101A THR* 3.0 13.2 + - - +
119A ILE* 1.3 70.9 - - - +
121A GLU* 1.3 59.0 + - - +
122A VAL 3.1 31.4 - - - +
123A LEU* 4.2 12.8 - - + -
130A LEU* 4.2 15.3 - - + -
131A SER 3.4 9.6 - - - +
132A PHE* 4.2 1.6 - - - -
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Residues in contact with GLU 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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99A VAL* 3.7 19.2 - - - +
119A ILE* 3.5 20.0 + - + +
120A LEU* 1.3 77.9 - - - +
122A VAL* 1.3 71.5 + - + +
131A SER* 2.9 19.6 + - - +
132A PHE 4.9 0.2 - - - -
133A ARG* 3.0 57.1 + - + +
145A ARG* 4.6 6.1 - - - -
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Residues in contact with VAL 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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40A HIS* 6.1 2.2 - - + +
99A VAL* 4.2 2.2 - - - -
120A LEU* 3.1 16.3 - - - +
121A GLU* 1.3 87.7 - - + +
123A LEU* 1.3 61.9 + - - +
124A ASP* 4.4 9.4 - - + +
129A ILE* 3.7 28.9 - - + +
130A LEU* 3.5 3.8 - - - -
131A SER* 3.1 35.2 + - - -
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Residues in contact with LEU 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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66A TRP* 3.9 26.2 - - + -
70A ARG* 4.3 17.0 - - + +
97A ILE* 4.3 33.7 - - + +
98A LYS* 5.0 4.5 - - - -
99A VAL* 3.8 19.6 - - + +
120A LEU* 4.2 9.4 - - + -
122A VAL* 1.3 74.5 - - - +
124A ASP* 1.3 59.0 + - - +
125A GLU* 3.6 27.2 + - + +
129A ILE 3.7 1.6 - - - -
130A LEU* 4.4 14.8 - - + -
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Residues in contact with ASP 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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40A HIS* 5.7 1.2 - - - -
66A TRP* 4.2 2.5 - - - -
122A VAL* 4.6 7.4 - - + -
123A LEU* 1.3 73.6 - - - +
125A GLU* 1.3 51.5 + - - +
126A GLU* 3.1 10.6 + - - +
127A LYS* 2.5 54.5 + - + +
128A ARG* 2.6 37.1 + - - -
129A ILE* 3.2 26.2 + - + +
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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