Contacts of the strand formed by residues 96 - 108 (chain L) 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 ILE 96 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92L LEU* 3.2 43.4 - - + +
93L ARG* 3.7 11.1 + - + +
94L ASP 3.4 0.4 - - - -
95L ASN* 1.3 98.3 - - - +
97L GLU* 1.3 66.0 + - - +
98L LYS 3.8 6.5 - - - +
99L VAL* 4.0 15.0 - - + -
120L TYR* 4.2 13.7 - - + -
121L HIS 3.7 7.6 - - - +
123L LYS* 4.1 8.6 + - - +
128L VAL* 3.6 30.1 - - + -
129L ASN* 4.0 13.5 - - - +
132L GLU* 4.2 10.8 - - - +
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Residues in contact with GLU 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L MET* 4.9 5.2 - - - +
87L PHE 4.2 6.2 - - - +
92L LEU* 3.4 19.2 - - - +
95L ASN 3.9 1.8 + - - -
96L ILE* 1.3 74.0 - - - +
98L LYS* 1.3 79.5 + - + +
121L HIS* 2.6 23.5 + - - +
122L PRO 3.7 12.6 - - - +
123L LYS* 3.7 29.9 - - + +
124L PRO* 5.3 3.8 - - + +
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Residues in contact with LYS 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73L ASP* 5.6 2.0 + - - -
85L THR* 3.8 26.9 + - + +
86L LEU 3.1 17.9 - - - +
87L PHE* 4.3 7.0 - - + -
92L LEU* 4.2 3.8 - - - -
96L ILE* 3.5 0.9 - - - +
97L GLU* 1.3 102.6 - - + +
99L VAL* 1.3 62.9 + - - +
100L VAL* 4.2 6.9 - - - +
121L HIS* 2.8 60.3 + - + +
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Residues in contact with VAL 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85L THR* 3.5 1.7 - - - -
86L LEU* 2.9 42.8 + - + +
92L LEU* 4.1 10.3 - - + -
96L ILE* 4.0 10.8 - - + -
98L LYS* 1.3 80.3 - - - +
100L VAL* 1.3 63.4 + - - +
101L TYR* 3.7 26.6 - - + +
118L VAL* 3.9 16.6 - - + -
119L THR 3.2 9.9 - - - +
120L TYR* 3.5 38.6 - - + -
132L GLU* 4.6 1.3 - - - +
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Residues in contact with VAL 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L LYS* 4.1 26.5 - - + -
84L TYR 3.6 9.4 - - - +
85L THR* 4.0 13.0 - - + +
98L LYS* 4.2 13.5 - - - +
99L VAL* 1.3 72.1 - - - +
101L TYR* 1.3 65.1 + - - +
102L GLU* 5.0 4.9 - - + +
117L THR* 3.5 3.1 - - + +
118L VAL* 3.2 5.8 - - - -
119L THR* 2.8 43.9 + - - +
121L HIS* 3.5 29.2 - - + +
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Residues in contact with TYR 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L ARG* 6.3 0.2 - - - -
70L HIS* 4.1 6.3 - + - -
82L CYS 4.1 0.4 - - - +
83L LYS* 3.3 4.7 - - - +
84L TYR* 2.8 84.9 + + + +
86L LEU* 4.0 13.1 - - + +
99L VAL* 3.7 30.4 - - + +
100L VAL* 1.3 72.4 - - - +
102L GLU* 1.3 59.4 + - - +
103L VAL* 4.4 6.1 - - + -
116L ILE* 5.6 0.7 - - + -
117L THR 3.8 3.4 - - - -
118L VAL* 3.7 28.0 - - + -
120L TYR* 4.7 2.4 + - - -
136L GLY* 5.9 0.5 - - - -
140L ALA* 5.6 3.1 - - + -
201L 2AN 3.3 47.0 + - - -
202L 2AN 4.5 15.9 - + + -
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Residues in contact with GLU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L TYR* 3.2 38.3 + - + +
82L CYS 3.4 5.2 - - - +
83L LYS* 3.8 24.1 - - + +
100L VAL* 5.2 5.0 - - + +
101L TYR* 1.3 74.2 - - - +
103L VAL* 1.3 64.5 + - - +
115L LYS 3.6 1.9 - - - +
116L ILE* 3.4 6.3 - - - +
117L THR* 2.9 55.3 + - + +
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Residues in contact with VAL 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L PHE* 4.8 0.7 - - + -
24L VAL* 4.1 16.2 - - + -
80L PHE 3.4 2.0 - - - +
81L TYR* 3.4 8.0 - - - -
82L CYS* 2.8 36.7 + - + +
84L TYR* 4.7 14.6 - - + -
101L TYR* 4.8 0.4 - - + -
102L GLU* 1.3 85.5 - - - +
104L LYS* 1.3 59.2 + - - +
105L LEU* 3.1 30.3 - - + -
115L LYS 3.8 2.2 - - - -
116L ILE* 4.2 9.6 - - + -
202L 2AN 3.3 41.3 - - + -
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Residues in contact with LYS 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L ASN* 3.0 34.6 + - - +
80L PHE* 3.5 1.1 - - - -
81L TYR* 3.7 30.7 - - + -
103L VAL* 1.3 74.4 - - - +
105L LEU* 1.3 76.6 + - - +
106L GLU* 4.8 7.4 - - + +
114L GLY* 2.9 25.1 - - - -
115L LYS* 3.1 23.6 + - + +
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Residues in contact with LEU 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L PRO* 4.1 11.4 - - + +
19L LEU* 3.7 41.1 - - + +
20L PHE* 3.9 17.9 - - + +
79L ASN 3.4 4.9 - - - +
80L PHE* 2.9 46.2 + - + +
103L VAL* 3.1 35.0 - - + -
104L LYS* 1.3 85.1 + - - +
106L GLU* 1.3 60.7 + - - +
112L SER* 5.3 2.0 - - - +
113L LYS 3.4 4.9 - - - +
114L GLY* 4.5 1.3 - - - -
115L LYS 5.5 0.4 - - - +
116L ILE* 5.7 0.2 - - + -
202L 2AN 4.1 24.9 - - + -
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Residues in contact with GLU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L PRO* 4.1 3.8 - - - -
80L PHE* 4.6 2.0 - - - -
104L LYS* 4.9 7.9 - - + +
105L LEU* 1.3 74.9 - - - +
107L ALA* 1.3 60.7 + - - +
108L VAL* 3.9 12.9 - - + +
112L SER* 3.3 8.5 - - - -
113L LYS* 2.7 70.0 + - + +
79P ASN* 5.6 3.6 + - - -
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Residues in contact with ALA 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L PRO* 3.3 29.6 - - + +
80L PHE* 4.8 1.4 - - - -
106L GLU* 1.3 76.5 - - - +
108L VAL* 1.3 66.6 + - - +
109L GLY 4.1 1.8 - - - +
111L GLY 3.5 2.0 - - - +
16P PRO* 5.2 1.6 - - + -
17P HIS* 6.2 2.0 - - - +
78P ALA 3.8 6.8 - - - +
80P PHE* 4.0 21.3 - - + -
107P ALA* 3.8 23.7 - - + +
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Residues in contact with VAL 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L GLU* 3.9 22.4 - - + +
107L ALA* 1.3 80.7 - - - +
109L GLY* 1.3 66.2 + - - +
110L GLY 3.1 0.5 + - - -
111L GLY* 2.8 24.0 + - - +
112L SER* 4.0 17.0 - - - +
113L LYS* 4.1 23.3 - - + +
78P ALA* 3.4 17.7 - - + +
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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