Contacts of the strand formed by residues 107 - 121 (chain A) in PDB entry 4N20
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 ASP 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.1 31.1 - - - -
12A GLY* 3.2 27.5 + - - -
34A PRO* 3.7 24.1 - - + +
96A ASN* 3.6 3.9 - - - +
97A TYR* 3.0 27.1 + - + +
105A PRO* 3.4 5.3 - - - +
106A ILE* 1.3 82.6 - - + +
108A GLN* 1.3 77.1 + - - +
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Residues in contact with GLN 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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12A GLY* 3.1 25.7 + - - -
13A SER 3.8 2.5 + - - +
94A THR* 3.7 22.5 + - + +
95A VAL 3.2 9.4 - - - +
96A ASN* 3.3 23.5 + - - +
97A TYR* 4.4 3.1 - - - -
107A ASP* 1.3 85.3 + - - +
109A ALA* 1.3 61.8 + - - +
110A GLY* 5.1 4.4 - - - +
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Residues in contact with ALA 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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9A LEU* 3.9 29.8 - - + +
10A GLN 3.8 17.5 - - - +
11A TYR* 4.1 5.8 - - - -
13A SER 3.7 4.9 - - - -
32A ALA* 4.1 0.7 - - + -
93A VAL 4.2 0.5 - - - +
94A THR* 3.8 0.8 - - - -
95A VAL* 2.8 33.7 + - - +
97A TYR* 4.0 16.3 - - + +
108A GLN* 1.3 76.9 - - - +
110A GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 110 (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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9A LEU* 4.1 7.0 - - - +
10A GLN 5.5 0.9 + - - +
13A SER 3.1 13.4 + - - +
14A ARG* 3.6 1.5 - - - -
15A VAL* 3.0 28.5 + - - +
93A VAL 3.6 6.7 - - - -
94A THR* 4.4 8.3 - - - -
108A GLN* 4.3 5.2 - - - +
109A ALA* 1.3 74.6 - - - +
111A LEU* 1.3 60.1 - - - +
112A PHE* 4.1 13.9 - - - -
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Residues in contact with LEU 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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7A VAL* 3.8 15.9 - - + -
9A LEU* 3.8 19.3 - - + +
15A VAL* 3.4 32.3 - - + +
17A ALA* 4.3 4.5 - - + -
25A LEU* 4.5 7.9 - - + -
27A THR* 4.2 19.7 - - + +
79A VAL* 4.7 9.2 - - + -
92A LYS* 3.2 6.1 - - - +
93A VAL* 2.8 48.8 + - + +
110A GLY* 1.3 74.1 - - - +
112A PHE* 1.3 61.6 + - - +
113A LEU* 4.0 32.8 + - + +
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Residues in contact with PHE 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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14A ARG* 3.3 66.2 - - + +
15A VAL 2.8 13.3 + - - +
16A GLU* 3.3 14.2 - - + +
17A ALA* 2.9 27.5 + - - +
91A ASP 3.8 4.5 - - - +
92A LYS* 4.1 29.6 - - + -
94A THR* 5.8 2.2 - - - -
110A GLY* 4.6 10.5 - - - -
111A LEU* 1.3 74.6 - - - +
113A LEU* 1.3 62.2 + - - +
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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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17A ALA* 3.3 19.5 - - + +
19A TYR* 4.5 7.6 - - + -
25A LEU* 3.9 23.6 - - + -
48A VAL* 4.2 12.6 - - + -
79A VAL* 3.9 26.0 - - + -
81A MET* 3.9 29.8 - - - -
85A SER* 4.2 0.3 + - - -
91A ASP* 2.9 34.3 + - + +
93A VAL* 4.8 4.0 - - + -
111A LEU* 4.0 25.6 - - + +
112A PHE* 1.3 76.0 - - - +
114A THR* 1.3 62.8 + - - +
115A ALA 4.1 0.4 - - - -
704A ACT 5.2 1.7 - - - +
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Residues in contact with THR 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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17A ALA 3.1 9.5 + - - -
18A VAL* 3.3 8.2 - - + +
19A TYR* 2.8 24.2 + - - +
85A SER* 3.6 3.8 - - - -
113A LEU* 1.3 74.5 + - - +
115A ALA* 1.3 61.2 + - - +
116A ILE* 4.3 6.3 - - + -
191A PRO* 3.7 34.5 - - + -
195A PRO* 3.6 35.1 - - + +
704A ACT 4.3 15.7 + - + +
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Residues in contact with ALA 115 (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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19A TYR* 3.2 11.2 - - + +
21A LEU* 4.0 10.3 - - + -
81A MET* 3.6 32.5 - - + +
83A GLN 3.6 16.6 - - - +
84A ALA* 3.5 4.0 - - - +
85A SER* 2.8 37.7 + - - +
113A LEU 4.1 0.8 - - - -
114A THR* 1.3 72.5 - - - +
116A ILE* 1.3 65.1 + - - +
191A PRO* 4.2 2.4 - - - +
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Residues in contact with ILE 116 (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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18A VAL* 3.7 26.5 - - + -
19A TYR 2.9 7.9 + - - +
20A VAL* 3.4 5.5 - - + +
21A LEU* 2.9 29.1 + - - -
84A ALA* 4.3 0.4 - - - -
114A THR* 4.3 11.4 - - + +
115A ALA* 1.3 80.3 - - - +
117A GLU* 1.3 61.8 + - - +
118A ILE* 3.4 33.7 - - + -
189A LYS 3.2 10.3 - - - +
190A GLY* 4.3 1.3 - - - -
191A PRO* 4.1 19.3 - - + -
194A LEU* 4.0 27.6 - - + -
195A PRO* 5.7 1.1 - - + -
200A ILE* 5.5 0.4 - - + -
241A TYR* 4.5 9.0 - - + +
272A LEU* 4.1 4.3 - - + -
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Residues in contact with GLU 117 (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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20A VAL* 5.2 0.2 - - - -
21A LEU* 3.9 27.9 - - + +
84A ALA* 4.3 0.2 - - - +
116A ILE* 1.3 74.9 - - - +
118A ILE* 1.3 70.4 + - - +
119A SER* 4.9 10.4 - - - -
132A LYS* 6.0 1.9 - - - +
187A ARG* 4.6 14.0 - - - +
188A THR* 3.1 24.6 - - - -
189A LYS* 2.8 39.4 + - + +
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Residues in contact with ILE 118 (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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20A VAL* 4.4 12.9 - - + +
21A LEU 5.5 1.7 + - - +
116A ILE* 3.4 34.3 + - + -
117A GLU* 1.3 81.6 - - - +
119A SER* 1.3 63.8 + - - +
186A LEU* 4.0 20.2 - - + -
187A ARG 3.5 2.9 - - - -
188A THR* 4.4 9.4 - - + -
200A ILE* 4.4 16.2 - - + -
241A TYR* 6.4 0.4 - - + -
270A VAL* 4.4 13.0 - - + -
271A SER 6.4 0.4 - - - -
272A LEU* 4.1 26.5 - - + +
286A PHE* 3.6 38.0 - - + -
288A ASP* 4.2 0.5 - - - +
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Residues in contact with SER 119 (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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117A GLU* 4.9 11.2 - - - -
118A ILE* 1.3 77.7 - - - +
120A LEU* 1.3 59.4 + - - +
121A ASP* 2.6 29.2 + - - +
133A ASN* 3.3 19.7 - - - +
137A LYS* 3.1 12.3 + - - -
185A ILE 3.4 2.9 - - - +
186A LEU* 3.5 4.6 - - - -
187A ARG* 2.9 42.9 + - - +
288A ASP* 3.5 5.1 + - - -
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Residues in contact with LEU 120 (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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119A SER* 1.3 69.1 - - - +
121A ASP* 1.3 58.8 + - - +
137A LYS* 2.7 28.4 + - - -
184A MET* 3.7 32.5 - - + -
185A ILE 3.7 4.3 - - - +
186A LEU* 4.1 20.1 - - + +
202A LEU* 4.0 29.4 - - + -
250A PHE* 5.0 1.8 - - + -
268A ILE 3.8 23.6 - - - +
270A VAL* 3.9 22.4 - - + +
288A ASP* 2.9 18.2 + - - +
290A VAL* 3.2 22.6 - - + +
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Residues in contact with ASP 121 (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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119A SER* 2.6 33.8 + - - -
120A LEU* 1.3 75.1 - - - +
122A VAL* 1.3 69.8 + - - +
130A VAL* 3.5 5.7 - - + +
131A GLU 3.6 5.4 - - - +
132A LYS* 3.6 1.6 - - - +
133A ASN* 3.1 26.8 + - - +
134A ASN 6.0 0.2 - - - +
137A LYS* 4.7 1.8 - - - +
184A MET* 3.4 1.7 - - - +
185A ILE 2.8 39.1 + - - +
187A ARG* 2.8 45.1 + - - +
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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