Contacts of the strand formed by residues 94 - 101 (chain A) 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 LEU 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A VAL* 4.5 10.3 - - + -
59A GLU 5.3 0.2 - - - +
61A MET* 4.7 7.2 - - + -
89A GLU* 2.6 34.8 + - - +
92A PRO* 4.0 5.2 - - - +
93A VAL* 1.3 77.8 - - + +
95A VAL* 1.3 63.5 + - - +
96A ARG 3.5 3.3 + - - -
124A LEU* 3.8 35.5 - - + +
125A ARG 3.1 8.7 - - - +
126A GLY* 3.4 30.7 - - - +
127A ARG 4.3 0.2 - - - +
134A VAL* 3.7 30.5 - - + -
153A ILE* 4.6 11.4 - - + -
155A ILE* 3.9 17.5 - - + -
194B VAL* 3.8 5.5 - - - +
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Residues in contact with VAL 95 (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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92A PRO* 4.7 2.2 - - + -
94A LEU* 1.3 73.1 - - - +
96A ARG* 1.3 66.2 + - - +
97A THR* 3.4 7.1 + - - +
124A LEU* 4.2 0.7 - - - -
125A ARG* 2.7 40.8 + - + +
127A ARG* 3.6 17.0 - - - +
162A PHE* 3.6 28.3 - - + -
164A ASP* 4.0 8.5 - - - +
192B HIS* 3.5 36.3 - - + +
193B PHE* 3.7 24.0 - - + -
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Residues in contact with ARG 96 (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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84A PHE* 3.9 13.9 - - - -
85A LEU 3.5 5.5 + - - -
86A ASN* 2.8 34.9 + - - +
87A ALA* 3.9 4.8 - - + +
94A LEU 3.5 4.0 + - - -
95A VAL* 1.3 69.8 - - - +
97A THR* 1.3 61.1 + - - +
98A ALA 4.0 7.4 - - - +
99A GLN* 2.9 35.1 + - - -
122A ILE* 4.2 6.7 - - + -
123A ASN 3.5 5.6 - - - -
124A LEU* 3.7 10.9 - - + +
190B GLY 4.8 2.4 + - - -
191B PHE* 3.0 61.2 + - + +
192B HIS* 3.1 35.6 + - - -
194B VAL* 3.8 25.9 - - + +
195B ARG 5.8 0.2 - - - +
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Residues in contact with THR 97 (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 GLU* 3.3 32.0 + - - +
95A VAL* 3.4 12.4 + - - +
96A ARG* 1.3 74.7 + - - +
98A ALA* 1.3 64.3 + - + +
105A PHE* 5.2 0.5 - - - -
123A ASN* 2.7 17.1 + - + +
125A ARG* 4.2 11.4 - - - +
164A ASP* 5.3 0.3 + - - -
178B GLN* 4.5 10.4 + - - -
179B HIS* 4.5 6.4 + - - +
188B LEU* 5.4 0.2 - - - +
191B PHE* 3.9 9.3 - - - -
192B HIS* 4.3 16.0 + - + +
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Residues in contact with ALA 98 (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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96A ARG* 3.7 3.4 - - - +
97A THR* 1.3 80.8 - - + +
99A GLN* 1.3 65.9 + - - +
100A PHE* 3.8 6.7 - - + -
105A PHE* 3.8 10.1 - - + -
122A ILE* 3.6 0.5 - - - -
123A ASN* 2.8 44.3 + - - +
179B HIS* 3.3 26.7 - - - +
191B PHE* 3.7 12.8 - - - -
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Residues in contact with GLN 99 (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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84A PHE* 3.8 11.9 - - - -
85A LEU* 2.9 47.9 + - + +
86A ASN* 3.9 1.4 + - - -
96A ARG* 2.9 31.0 + - - +
98A ALA* 1.3 78.2 - - - +
100A PHE* 1.3 70.4 + - - +
105A PHE* 3.3 6.5 - - - -
106A ALA* 2.6 49.1 + - - +
121A SER 3.1 13.0 - - - +
122A ILE* 4.0 9.7 - - + +
191B PHE* 3.7 14.7 - - + -
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Residues in contact with PHE 100 (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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85A LEU* 3.4 3.9 - - - +
98A ALA* 3.8 21.8 - - + -
99A GLN* 1.3 77.2 - - - +
101A ILE* 1.3 64.0 + - - +
103A GLU* 5.5 3.8 - - - -
104A GLN* 2.9 10.5 - - - +
105A PHE* 3.4 37.7 - + + -
106A ALA 4.3 0.7 - - - +
119A ALA 4.6 0.4 - - - -
120A PHE* 3.0 7.8 - - - +
121A SER* 2.8 46.4 + - - +
123A ASN* 3.9 14.8 - - - -
179B HIS* 3.4 32.8 - + + -
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Residues in contact with ILE 101 (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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67A VAL* 4.7 1.8 - - + -
85A LEU* 4.4 11.7 - - + -
100A PHE* 1.3 77.4 - - - +
102A GLY* 1.3 66.3 + - - +
103A GLU 3.0 1.5 - - - +
104A GLN* 2.7 27.2 + - - +
106A ALA* 3.7 22.7 - - + -
110A VAL* 4.1 13.9 - - + -
112A LEU* 4.5 11.4 - - + -
118A TYR* 4.0 16.4 - - + -
119A ALA 3.3 13.2 - - - +
120A PHE* 3.8 18.8 - - + -
138A ILE* 4.1 25.6 - - + -
268A LEU* 3.6 20.2 - - + +
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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