Contacts of the strand formed by residues 125 - 130 (chain A) in PDB entry 1WS6
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 PHE 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 3.2 54.7 - - + +
59A PHE 3.9 0.9 - - - -
60A LEU* 3.6 43.3 - - + -
81A VAL* 3.7 29.6 - - + -
114A PHE* 4.5 9.6 - + - -
123A GLU* 4.1 17.5 - - + -
124A ARG* 1.3 77.6 - - - +
126A THR* 1.3 61.1 + - - +
127A VAL 3.8 12.3 - - - +
150A LEU* 3.0 27.8 + - + +
151A VAL* 3.2 10.5 - - + -
152A GLU* 2.9 29.6 + - - +
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Residues in contact with THR 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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53A TYR* 3.7 34.1 - - + -
56A ARG 4.0 10.2 + - - +
57A GLY* 3.8 6.2 - - - -
58A ARG 2.8 20.2 + - - +
78A TRP* 3.9 14.1 - - + -
125A PHE* 1.3 74.0 - - - +
127A VAL* 1.3 60.5 + - + +
151A VAL* 3.5 1.7 - - - +
152A GLU* 2.8 29.9 + - - +
154A GLY 5.6 0.2 - - - -
155A GLY* 3.0 10.2 - - - -
156A LEU 2.9 24.4 + - - -
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Residues in contact with VAL 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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49A LEU* 4.6 9.6 - - + -
53A TYR* 3.9 18.6 - - + -
58A ARG 3.2 4.2 + - - +
59A PHE* 3.4 33.8 - - + -
60A LEU* 2.8 26.5 + - - +
78A TRP* 3.6 27.6 - - + -
125A PHE* 3.5 3.4 - - - +
126A THR* 1.3 85.3 - - - +
128A ALA* 1.3 71.3 + - - +
129A PHE* 4.1 1.3 - - + +
151A VAL* 4.5 0.9 - - - -
156A LEU* 3.3 12.1 - - + +
158A VAL* 4.5 15.7 - - + -
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Residues in contact with ALA 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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60A LEU* 3.4 28.0 - - + +
62A PRO* 5.6 0.4 - - + -
125A PHE* 5.4 0.7 - - + -
127A VAL* 1.3 77.6 - - - +
129A PHE* 1.3 59.3 + - - +
130A MSE 4.0 0.2 + - - -
145A LEU* 4.2 14.0 - - + +
150A LEU* 6.1 0.7 - - + -
151A VAL* 3.7 20.9 - - + -
156A LEU 2.9 8.9 + - - -
157A TYR* 3.4 14.1 - - + -
158A VAL 2.9 26.0 + - - +
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Residues in contact with PHE 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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37A SER* 5.9 1.1 - - - -
41A LEU* 4.9 4.3 - - + -
42A ARG* 6.5 0.9 - - + -
45A LEU* 3.6 30.1 - - + -
59A PHE* 3.5 24.5 - - + -
60A LEU 2.9 7.3 + - - +
61A ASP* 3.5 7.7 - - - +
62A PRO* 3.0 22.0 - - - +
69A VAL* 3.5 40.2 - - + -
127A VAL* 4.1 2.5 - - + +
128A ALA* 1.3 72.9 - - - +
130A MSE 1.3 62.3 + - - +
131A ALA* 3.3 35.9 - - + -
158A VAL* 3.4 19.1 - - + -
160A GLN* 3.6 16.2 - - + -
180A LEU* 4.1 19.7 - - + -
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Residues in contact with MSE 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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62A PRO* 3.3 33.7 - - + -
63A PHE* 3.4 30.3 - - + -
111A VAL* 3.8 11.2 - - + -
115A LEU* 5.5 0.7 - - + -
128A ALA 4.0 0.2 + - - -
129A PHE* 1.3 78.4 - - - +
131A ALA* 1.3 60.5 + - - +
132A PRO* 3.3 20.8 - - + +
141A LEU* 4.1 20.4 - - + +
142A PHE* 3.9 23.4 - - + -
145A LEU* 4.0 31.0 - - + -
158A VAL 2.9 12.0 + - - +
159A LEU* 3.6 2.9 - - + -
160A GLN 2.9 25.1 + - - -
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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