Contacts of the strand formed by residues 126 - 131 (chain A) in PDB entry 3JW8
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.4 22.2 - - + +
83A PHE* 4.7 6.7 - - + -
114A VAL* 4.2 16.4 - - + -
118A GLN* 3.1 44.4 - - + +
124A LEU 3.8 4.0 - - - +
125A PRO* 1.4 76.2 - - - +
127A PHE* 1.3 73.4 + - - +
148A HIS* 4.9 6.6 + - + +
149A PHE* 3.5 30.0 - - + -
150A ALA* 2.9 25.1 + - - +
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Residues in contact with PHE 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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53A ALA* 4.0 13.5 - - + -
54A LEU 2.8 14.1 + - - +
55A ILE* 3.3 25.7 - - + -
56A PHE 3.0 22.7 + - - -
80A LEU* 4.3 6.5 - - + -
125A PRO* 4.3 4.7 - - + -
126A VAL* 1.3 81.4 - - - +
128A LEU* 1.3 64.9 + - - +
150A ALA* 3.8 20.2 - - + -
151A GLY* 3.3 35.4 - - - -
153A VAL* 6.0 0.9 - - + -
299A TRP* 4.1 15.5 - + - -
300A VAL* 5.0 9.0 - - + -
303A ARG* 3.6 35.9 - - + -
304A THR* 3.5 24.7 - - + -
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Residues in contact with LEU 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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55A ILE* 4.2 5.5 - - - +
56A PHE* 3.5 24.2 - - + +
58A SER* 6.5 0.4 - - - -
110A VAL* 4.4 15.9 - - + -
114A VAL* 4.6 1.1 - - + -
127A PHE* 1.3 78.7 - - - +
129A LEU* 1.4 59.1 + - - +
130A GLY 4.3 0.2 - - - -
138A ALA* 3.5 42.2 - - + +
141A THR* 4.1 11.7 - - + -
142A ALA* 4.1 9.0 - - + +
149A PHE* 3.7 42.2 - - + -
151A GLY 3.0 7.5 + - - +
152A MSE 3.2 11.3 - - + -
153A VAL* 2.8 24.9 + - - +
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Residues in contact with LEU 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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55A ILE* 4.2 13.7 - - + -
56A PHE 2.9 12.4 + - - +
57A VAL* 3.5 24.3 - - + -
58A SER* 2.8 28.4 + - - -
68A TYR* 4.4 15.0 - - + -
71A LEU* 4.5 7.2 - - + -
75A LEU* 4.3 21.8 - - + -
128A LEU* 1.4 73.7 - - - +
130A GLY* 1.3 64.5 + - - +
138A ALA* 4.9 2.2 - - - -
153A VAL* 3.2 31.4 - - + +
155A ILE* 4.2 17.5 - - + -
296A ILE* 4.4 18.4 - - + -
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Residues in contact with GLY 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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58A SER* 3.5 8.7 - - - -
129A LEU* 1.3 79.1 - - - +
131A HIS* 1.3 61.3 + - - -
134A GLY 3.6 15.9 - - - -
135A GLY* 3.8 10.1 - - - -
138A ALA* 4.5 4.9 - - - +
153A VAL 2.9 7.9 + - - +
154A LEU* 3.5 5.2 - - - -
155A ILE* 2.9 25.2 + - - +
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Residues in contact with HIS 131 (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 SER 3.3 6.7 + - - -
60A GLY* 3.7 8.1 + - - -
63A GLU* 3.7 8.3 - - - -
68A TYR* 3.2 31.9 - - + +
129A LEU* 5.1 0.4 - - - +
130A GLY* 1.3 74.4 - - - +
132A SER* 1.4 70.9 + - - +
134A GLY* 3.0 18.5 + - - -
135A GLY 3.6 0.8 - - - +
155A ILE* 2.9 27.7 + - + +
156A SER* 3.5 14.2 + - - -
279A HIS* 3.5 30.5 - + - -
280A VAL* 4.2 3.2 - - + +
282A HIS* 3.7 28.0 - + + -
866A MRD 2.8 33.5 + - + -
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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