Contacts of the strand formed by residues 111 - 122 (chain P) in PDB entry 4N3E
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 111 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205L 2AN 4.9 0.2 + - - -
12P SER 3.4 13.9 - - - -
13P PRO* 3.7 12.0 + - - +
14P ILE 3.7 3.6 - - - -
15P ALA* 4.0 1.8 - - - -
16P PRO* 3.5 9.5 - - - +
107P ALA* 3.5 0.2 - - - -
108P VAL 2.7 38.3 + - - -
109P GLY 4.3 0.7 - - - +
110P GLY* 1.3 81.9 - - - +
112P SER* 1.3 59.5 + - - -
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Residues in contact with SER 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P GLU* 3.5 1.6 - - - -
12P SER* 2.9 37.1 + - - -
14P ILE 2.6 21.7 + - - -
16P PRO* 3.6 26.4 - - - -
19P LEU* 3.3 20.1 - - - +
105P LEU* 4.8 4.2 - - - +
106P GLU 3.4 6.1 - - - -
108P VAL* 4.4 2.0 - - - +
111P GLY* 1.3 76.3 - - - -
113P LYS* 1.3 65.9 + - - +
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Residues in contact with LYS 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P GLU 3.4 7.0 - - - +
11P GLU* 3.7 35.2 - - + +
105P LEU* 3.4 7.3 - - - +
106P GLU* 3.0 56.6 + - + +
108P VAL* 3.9 30.3 - - + +
112P SER* 1.3 74.9 - - - +
114P GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P GLU* 3.3 11.2 - - - +
10P GLU* 2.9 34.1 + - - +
104P LYS 3.5 9.4 - - - -
105P LEU* 3.9 11.2 - - - -
106P GLU* 5.8 0.4 - - - -
113P LYS* 1.3 77.0 - - - +
115P LYS* 1.3 60.2 + - - +
116P ILE* 4.1 7.9 - - - -
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Residues in contact with LYS 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O LYS* 5.6 5.3 - - - +
7P VAL* 4.5 22.8 - - + +
8P LYS 3.4 8.3 - - - +
9P GLU* 3.7 26.5 - - - +
102P GLU* 3.6 5.6 - - - +
103P VAL 3.9 0.2 - - - -
104P LYS* 2.9 40.4 + - + +
114P GLY* 1.3 73.9 - - - +
116P ILE* 1.3 64.8 + - - +
117P THR* 4.3 17.2 - - + +
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Residues in contact with ILE 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P ILE 3.8 0.9 - - - +
7P VAL* 3.5 1.7 - - - -
8P LYS* 2.9 50.5 + - + +
10P GLU* 4.5 17.7 - - + -
101P TYR* 5.6 3.4 - - + -
102P GLU 3.2 6.5 - - - +
103P VAL* 4.2 25.1 - - + -
105P LEU* 4.5 9.4 - - + -
114P GLY* 4.1 18.2 - - - -
115P LYS* 1.3 79.4 - - - +
117P THR* 1.3 67.0 + - - +
118P VAL* 4.2 20.6 - - + -
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Residues in contact with THR 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P THR* 4.3 6.0 - - - +
6P ILE 3.2 9.4 - - - -
7P VAL* 3.8 22.0 - - + -
100P VAL 3.4 1.0 + - - +
101P TYR* 3.3 3.5 - - - -
102P GLU* 2.7 64.5 + - + +
115P LYS* 4.3 20.6 - - - +
116P ILE* 1.3 80.0 - - - +
118P VAL* 1.3 64.5 + - - +
119P THR* 4.0 11.8 + - - -
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Residues in contact with VAL 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P TYR 3.8 1.4 - - - +
5P THR* 3.1 3.6 - - - +
6P ILE* 2.7 44.4 + - + +
8P LYS* 5.1 4.9 - - - +
99P VAL* 3.4 27.1 - - + -
100P VAL 3.2 2.5 - - - +
101P TYR* 3.5 33.9 - - + -
116P ILE* 4.2 15.5 - - + -
117P THR* 1.3 79.2 - - - +
119P THR* 1.3 65.0 + - - +
120P TYR* 4.0 15.9 - - + +
137P GLU* 5.1 13.7 - - - +
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Residues in contact with THR 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O THR* 5.4 5.2 - - + -
7O VAL* 5.9 3.8 - - + -
3P ALA* 4.4 10.3 - - + -
4P TYR 3.3 3.1 - - - +
5P THR* 3.1 28.4 - - + +
98P LYS 3.8 0.7 - - - +
99P VAL* 3.2 5.5 - - - +
100P VAL* 2.7 54.1 + - - +
117P THR* 4.0 7.1 + - - -
118P VAL* 1.3 73.6 - - - +
120P TYR* 1.3 64.2 + - - +
121P HIS* 3.9 21.5 + - + +
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Residues in contact with TYR 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P ALA* 3.0 16.6 - - - +
4P TYR* 2.5 38.4 + - + +
6P ILE* 4.9 4.3 - - + -
96P ILE* 4.3 16.8 - - + -
98P LYS 3.9 2.0 - - - -
99P VAL* 3.8 34.5 - - + +
101P TYR* 5.0 1.4 + - - -
118P VAL* 4.0 17.4 - - + +
119P THR* 1.3 76.7 - - - +
121P HIS* 1.3 61.0 + - - +
122P PRO* 2.9 14.4 - - - +
128P VAL* 4.2 9.4 - - + -
132P GLU* 3.5 30.7 + - + -
133P VAL* 3.7 34.5 + - + -
136P GLY* 3.7 18.0 + - - -
137P GLU* 4.7 2.2 + - - -
201P 2AN 4.1 14.3 - + - -
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Residues in contact with HIS 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O VAL* 4.9 19.4 - - + +
3P ALA* 4.3 12.9 - - + +
96P ILE* 3.6 6.4 - - - +
97P GLU* 2.7 36.9 + - + -
98P LYS* 2.6 57.6 + - + +
100P VAL* 3.5 26.7 - - + +
119P THR* 3.9 22.4 + - + +
120P TYR* 1.3 71.6 - - - +
122P PRO* 1.4 58.6 - - + +
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Residues in contact with PRO 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P MET* 4.8 12.1 - - - +
2P ALA 3.7 19.5 - - - +
3P ALA* 3.9 8.5 - - + -
95P ASN 3.5 6.7 - - - +
96P ILE* 4.6 1.1 - - + -
97P GLU* 3.9 5.6 - - - +
120P TYR 2.9 13.0 - - - +
121P HIS* 1.4 89.0 - - + +
123P LYS* 1.3 69.0 + - - +
124P PRO* 3.9 1.0 - - - +
126P CYS* 4.3 19.7 - - + +
127P THR* 4.4 2.9 - - - +
128P VAL* 3.5 26.7 - - + +
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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