Contacts of the strand formed by residues 104 - 114 (chain A) in PDB entry 4ZIN
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 4.9 5.8 - - + -
97A MET 3.3 9.4 - - - +
98A ASN* 3.6 18.4 - - - +
99A PHE* 4.5 0.2 - - - -
102A GLY 3.5 11.2 - - - +
103A GLY* 1.3 80.8 - - - +
105A VAL* 1.3 65.8 + - - +
106A THR* 4.1 22.7 - - + -
125A ARG* 3.7 4.4 - - - +
126A GLY* 3.2 2.8 - - - -
127A THR* 2.8 49.6 + - - +
128A ASN* 5.1 3.4 - - + +
129A PHE* 3.9 1.5 - - - -
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Residues in contact with VAL 105 (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 ILE* 4.5 14.1 - - + +
64A GLN* 4.7 0.7 - - - +
95A ARG 3.9 0.3 - - - +
96A VAL* 3.5 3.3 - - - -
97A MET* 2.8 56.3 + - + +
99A PHE* 3.7 19.0 - - + -
104A VAL* 1.3 79.2 - - - +
106A THR* 1.3 66.5 + - - +
107A VAL* 3.6 24.0 - - + -
124A LEU* 3.8 23.1 - - + -
125A ARG 3.3 4.3 - - - +
126A GLY* 4.0 8.7 - - - -
129A PHE* 3.8 12.8 - - + -
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Residues in contact with THR 106 (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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95A ARG 3.3 6.7 - - - -
96A VAL* 4.3 17.9 - - + -
104A VAL* 4.1 14.1 - - + -
105A VAL* 1.3 78.7 - - - +
107A VAL* 1.3 65.9 + - - +
124A LEU* 3.5 0.2 - - - -
125A ARG* 2.9 69.6 + - - +
301A SO4 3.0 18.8 + - - -
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Residues in contact with VAL 107 (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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64A GLN* 3.7 23.3 - - + +
93A TRP* 3.6 25.7 - - + -
94A GLU* 3.3 4.2 - - - +
95A ARG* 2.8 42.0 + - + +
97A MET* 5.1 0.2 - - - -
105A VAL* 3.6 20.2 - - + -
106A THR* 1.3 82.8 - - - +
108A THR* 1.3 70.6 + - - +
122A VAL* 3.5 24.7 - - + -
123A LYS 3.3 13.0 - - - +
124A LEU* 4.0 5.2 - - + -
301A SO4 3.8 0.9 + - - -
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Residues in contact with THR 108 (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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93A TRP 3.3 6.5 - - - +
94A GLU* 4.0 25.6 - - + +
107A VAL* 1.3 81.7 - - - +
109A GLN* 1.3 64.3 + - - +
121A LYS 4.0 0.2 - - - +
122A VAL* 3.4 3.1 - - - +
123A LYS* 2.9 47.2 + - - +
301A SO4 3.1 22.0 + - - +
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Residues in contact with GLN 109 (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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64A GLN 5.3 0.4 + - - -
66A CH6 3.5 18.6 + - - -
91A PHE 4.4 0.9 - - - +
92A LYS* 3.2 9.0 - - - +
93A TRP* 2.9 72.6 + - + +
108A THR* 1.3 77.8 - - - +
110A ASP* 1.3 69.7 + - - +
111A SER* 2.7 30.8 + - - -
120A TYR* 3.5 25.1 - - - +
121A LYS 3.3 11.7 - - - +
122A VAL* 3.8 14.7 - - + +
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PHE 3.9 2.7 - - - -
92A LYS* 2.9 32.7 + - + +
109A GLN* 1.3 78.5 - - - +
111A SER* 1.3 64.3 + - - +
112A SER* 4.1 6.6 + - - -
119A ILE 3.5 1.2 - - - +
120A TYR* 3.3 5.5 - - - -
121A LYS* 2.9 43.3 + - + +
184A LYS* 3.0 22.7 + - - -
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Residues in contact with SER 111 (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 CH6 4.9 0.3 + - - -
87A PHE* 4.3 5.6 - - - -
90A GLY* 3.2 2.1 - - - -
91A PHE* 2.9 64.3 + - - -
109A GLN* 2.7 31.8 + - - -
110A ASP* 1.3 72.2 + - - +
112A SER* 1.3 60.8 + - - +
119A ILE 3.5 4.0 - - - -
120A TYR* 3.5 15.2 - - - -
184A LYS* 3.1 8.5 + - - -
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Residues in contact with SER 112 (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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87A PHE* 3.8 9.5 - - - -
89A GLU 3.8 9.6 - - - -
110A ASP* 4.1 6.0 + - - -
111A SER* 1.3 75.5 - - - +
113A LEU* 1.3 64.1 + - - +
114A GLN* 4.5 11.4 + - - +
118A PHE* 3.3 6.1 - - - +
119A ILE* 2.8 47.9 + - - +
184A LYS* 3.9 12.8 - - - -
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Residues in contact with LEU 113 (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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7A ILE* 3.8 37.0 - - + +
8A ILE* 4.6 1.8 - - + -
12A MET* 3.7 21.5 - - + -
87A PHE* 3.9 7.2 - - + -
88A PRO* 3.5 28.6 + - + +
112A SER* 1.3 76.8 - - - +
114A GLN* 1.3 77.4 + - - +
115A ASP 4.3 0.4 - - - +
116A GLY* 3.8 9.6 - - - +
117A GLU 3.4 32.1 - - - +
118A PHE* 4.0 10.5 - - + +
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Residues in contact with GLN 114 (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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112A SER* 4.5 12.4 + - - +
113A LEU* 1.3 86.1 + - - +
115A ASP* 1.3 83.8 + - - +
116A GLY 3.1 1.6 - - - -
117A GLU* 2.8 25.5 + - - +
119A ILE* 3.8 18.2 - - + -
169B ASP 3.7 20.6 - - - +
170B GLY* 4.1 4.2 - - - -
171B GLY 4.5 2.1 + - - -
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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