Contacts of the strand formed by residues 144 - 156 (chain I) in PDB entry 4PHZ
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 144 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B LEU* 4.0 5.8 - - - +
211B ARG* 3.8 17.7 - - - +
139I ASN* 3.3 6.0 - - - -
140I VAL 2.8 36.5 + - - -
141I GLU 4.6 0.4 + - - -
143I GLY* 1.3 75.1 - - - +
145I PRO* 1.3 73.7 - - - +
146I ILE* 3.7 1.6 + - - +
201J TYR* 5.2 1.8 - - - -
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Residues in contact with PRO 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.9 19.5 - - - +
211B ARG* 4.5 12.6 - - + +
213B PHE* 5.4 1.8 - - + -
34I GLN* 3.5 20.4 + - - +
137I GLN* 4.4 4.7 - - - +
139I ASN* 3.0 21.5 - - - +
144I GLY* 1.3 84.0 - - - +
146I ILE* 1.3 64.1 - - - +
147I ILE* 4.0 10.5 - - + -
196J THR 5.6 0.4 - - - +
137K ILE* 3.5 34.5 - - + -
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Residues in contact with ILE 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.6 25.6 - - + -
34I GLN* 4.9 1.1 - - - +
39I ARG* 5.4 9.2 - - + +
42I THR* 3.9 31.0 - - + +
43I LEU* 4.0 33.0 - - + +
45I TRP* 3.6 12.7 - - - +
73I TRP* 4.4 4.0 - - + -
137I GLN* 3.5 4.5 - - - +
138I ILE 2.7 40.0 + - - +
140I VAL* 3.8 28.9 - - + -
144I GLY 4.3 0.7 - - - +
145I PRO* 1.3 77.7 - - - +
147I ILE* 1.3 65.8 + - - +
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Residues in contact with ILE 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I HIS 5.2 2.7 - - - +
30I GLY 5.5 0.9 - - - +
31I GLU* 3.6 33.9 - - + +
34I GLN* 3.4 22.1 + - - +
39I ARG* 6.1 1.4 - - - +
45I TRP* 3.7 9.6 + - - -
88I GLY* 5.9 0.4 - - - -
135I HIS* 3.2 38.4 - - + +
136I ALA 4.0 1.6 - - - +
137I GLN* 3.8 22.9 - - + +
145I PRO* 4.0 9.9 - - + -
146I ILE* 1.3 74.9 - - - +
148I GLY* 1.3 63.1 + - - +
322I ALA 4.4 8.1 - - - +
137K ILE* 4.0 30.7 - - + -
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Residues in contact with GLY 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I GLU* 5.3 1.0 - - - -
45I TRP* 3.4 20.9 - - - -
135I HIS* 2.9 23.7 + - - -
136I ALA 2.5 21.8 + - - -
147I ILE* 1.3 75.6 - - - +
149I PRO* 1.3 72.9 - - - +
322I ALA 5.3 2.5 - - - -
341I TYR* 4.4 0.5 + - - -
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Residues in contact with PRO 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I TRP* 3.7 24.0 - - + +
48I VAL* 3.7 21.5 - - + +
50I TRP* 3.4 20.5 - - + -
135I HIS* 3.4 0.6 - - - -
136I ALA* 3.2 23.4 + - + +
148I GLY* 1.3 83.3 - - - +
150I GLY* 1.3 59.1 + - - +
323I GLY* 3.8 22.7 - - - -
338I PHE* 3.9 19.5 - - + -
341I TYR* 3.8 0.7 - - - +
342I LEU* 3.6 20.6 - - + -
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Residues in contact with GLY 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I TRP* 3.6 2.7 - - - -
133I HIS* 3.4 7.4 - - - -
134I VAL 3.0 13.0 - - - -
135I HIS* 3.5 18.2 + - - -
149I PRO* 1.3 73.3 - - - +
151I GLN* 1.3 60.9 + - - -
339I PRO* 3.3 12.3 - - - +
341I TYR* 2.9 32.1 + - - -
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Residues in contact with GLN 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I TRP* 3.3 39.1 - - + +
53I THR* 4.3 15.3 - - + +
133I HIS* 3.4 8.9 + - - -
134I VAL 3.0 23.2 + - - +
150I GLY* 1.3 74.6 - - - +
152I TRP* 1.3 104.0 + - - +
153I ILE* 3.4 9.5 - - + +
337I ASP* 5.4 4.2 + - - -
338I PHE 4.6 0.8 - - - -
339I PRO* 3.3 39.8 - - - +
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Residues in contact with TRP 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I HIS* 3.9 19.7 - + - -
53I THR* 3.8 11.7 - - - +
131I ARG* 3.2 81.9 - - + +
132I TRP* 3.2 18.4 - - - -
133I HIS* 3.3 40.5 + + + -
151I GLN* 1.3 95.7 + - - +
153I ILE* 1.3 67.3 + - - +
154I GLU 4.1 1.3 - - - +
341I TYR* 5.8 2.2 - + - -
48K ARG* 5.4 2.5 - - - -
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Residues in contact with ILE 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I TRP* 3.8 23.3 - - + -
52I LYS 3.6 20.9 - - - +
53I THR* 3.6 10.5 - - - -
54I THR 4.7 0.4 - - - +
55I VAL* 4.3 16.2 - - + -
61I MET* 4.3 15.5 - - - -
94I LEU* 4.4 14.1 - - + -
130I GLY 3.7 2.3 - - - +
131I ARG* 4.7 0.9 - - - -
132I TRP* 2.8 34.6 + - - +
134I VAL* 3.7 23.8 - - + -
151I GLN* 3.4 15.9 - - + +
152I TRP* 1.3 84.3 - - - +
154I GLU* 1.3 71.0 + - - +
155I ILE* 3.7 1.5 + - + -
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Residues in contact with GLU 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I THR 3.0 15.7 + - - +
54I THR* 3.3 14.0 + - - +
55I VAL* 3.0 25.4 + - - +
130I GLY 3.4 12.8 - - - +
131I ARG* 4.3 25.6 + - - +
152I TRP 4.1 0.8 - - - -
153I ILE* 1.3 74.2 - - - +
155I ILE* 1.3 65.6 + - - +
156I LYS* 3.2 33.8 + - - +
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Residues in contact with ILE 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I VAL* 3.1 20.0 - - + +
57I VAL* 3.9 29.2 - - + +
93I VAL 3.6 21.1 - - - +
94I LEU* 3.8 22.4 - - + -
126I GLY* 4.3 2.7 - - - -
127I ARG 4.2 7.0 - - - +
128I ARG 3.6 17.0 - - - +
129I ALA* 3.3 4.6 - - - +
130I GLY 2.9 27.4 + - - +
132I TRP* 3.3 26.9 - - + -
153I ILE* 4.0 5.8 - - + +
154I GLU* 1.3 82.6 - - - +
156I LYS* 1.3 69.0 + - - +
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Residues in contact with LYS 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I THR* 4.5 16.8 - - + -
55I VAL 2.9 10.2 + - - +
56I ASN* 3.2 20.7 - - - +
57I VAL* 2.8 28.8 + - - +
129I ALA* 4.6 1.6 - - - -
154I GLU* 3.2 40.9 + - - +
155I ILE* 1.3 77.9 + - - +
157I GLY* 1.3 59.8 + - - +
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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