Contacts of the strand formed by residues 96 - 108 (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 ILE 96 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92P LEU* 3.5 43.3 - - + +
93P ARG 2.8 17.9 + - - +
94P ASP 3.4 0.6 - - - -
95P ASN* 1.3 88.7 - - - +
97P GLU* 1.3 64.1 + - - +
98P LYS 3.9 11.2 - - - +
99P VAL* 4.0 10.5 - - + -
120P TYR* 4.3 12.3 - - + -
121P HIS 3.6 9.6 - - - +
123P LYS* 3.3 15.1 - - - -
128P VAL* 4.2 22.9 - - + -
132P GLU* 3.5 35.0 - - + +
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Residues in contact with GLU 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P PHE* 4.2 11.3 - - - +
92P LEU* 4.1 13.8 - - - +
95P ASN 3.8 2.6 + - - -
96P ILE* 1.3 75.3 - - - +
98P LYS* 1.3 70.5 + - + +
121P HIS* 2.7 19.8 + - + +
122P PRO 3.9 13.2 - - - +
123P LYS* 3.9 28.2 + - + +
124P PRO* 4.5 7.9 - - + +
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Residues in contact with LYS 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P ASP* 5.6 1.4 + - - -
85P THR* 3.7 22.2 + - + +
86P LEU 3.2 15.0 - - - +
87P PHE* 4.4 6.1 - - + -
92P LEU* 4.2 2.7 - - - -
96P ILE* 3.8 1.8 - - - +
97P GLU* 1.3 91.2 - - + +
99P VAL* 1.3 63.4 + - - +
100P VAL* 3.9 13.0 - - + +
121P HIS* 2.6 73.7 + - + +
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Residues in contact with VAL 99 (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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85P THR* 3.4 1.3 - - - -
86P LEU* 2.7 53.3 + - + +
92P LEU* 4.2 8.7 - - + -
96P ILE* 4.0 11.7 - - + -
98P LYS* 1.3 78.4 - - - +
100P VAL* 1.3 63.0 - - - +
101P TYR* 3.7 16.9 - - + +
118P VAL* 3.4 28.7 - - + -
119P THR 3.2 7.6 - - - +
120P TYR* 3.8 34.1 - - + -
201P 2AN 4.5 4.7 - - + -
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Residues in contact with VAL 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P ASP* 4.8 0.9 - - - +
83P LYS* 4.1 29.8 - - + -
84P TYR 3.5 9.6 - - - +
85P THR* 3.6 21.1 - - + +
98P LYS* 3.9 12.3 - - - +
99P VAL* 1.3 73.7 - - - +
101P TYR* 1.3 64.5 + - - +
102P GLU* 5.7 0.9 - - + -
117P THR* 3.4 1.2 + - - +
118P VAL* 3.2 3.4 - - - -
119P THR* 2.7 53.1 + - - +
121P HIS* 3.5 27.8 - - + +
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Residues in contact with TYR 101 (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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27P ARG* 5.5 3.1 - - - -
70P HIS* 4.5 6.3 + - - -
82P CYS 3.9 0.3 - - - +
83P LYS* 3.2 5.2 - - - +
84P TYR* 2.8 87.4 + + + +
86P LEU* 4.5 10.9 - - + +
99P VAL* 3.7 31.1 - - + +
100P VAL* 1.3 75.6 - - - +
102P GLU* 1.3 60.0 + - - +
103P VAL* 4.2 4.5 - - + -
116P ILE* 5.6 3.6 - - + -
117P THR 3.3 4.9 - - - -
118P VAL* 3.5 29.1 - - + +
120P TYR* 5.0 1.6 + - - -
201P 2AN 3.3 47.2 + - - -
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Residues in contact with GLU 102 (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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81P TYR* 3.6 33.7 + - + +
82P CYS 3.3 6.3 - - - +
83P LYS* 4.0 23.2 + - + -
100P VAL* 5.7 1.3 - - + -
101P TYR* 1.3 73.0 - - - +
103P VAL* 1.3 61.8 + - - +
104P LYS* 6.5 0.2 - - + -
115P LYS* 3.6 4.7 - - - +
116P ILE* 3.2 6.3 - - - +
117P THR* 2.7 61.7 + - + +
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Residues in contact with VAL 103 (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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20P PHE* 4.0 13.5 - - + -
23P LEU 5.7 0.4 - - - +
24P VAL* 3.7 32.3 - - + -
81P TYR* 3.3 6.2 - - - -
82P CYS* 2.7 42.8 + - + +
84P TYR* 4.4 17.0 - - + +
101P TYR* 5.1 2.5 - - + -
102P GLU* 1.3 76.0 - - - +
104P LYS* 1.3 65.3 + - - +
105P LEU* 4.1 17.3 - - + -
115P LYS 3.9 2.5 - - - -
116P ILE* 4.2 19.7 - - + -
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Residues in contact with LYS 104 (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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79P ASN* 2.5 41.5 + - - +
80P PHE 3.1 7.2 - - - +
81P TYR* 3.9 25.6 - - + -
103P VAL* 1.3 76.9 - - - +
105P LEU* 1.3 82.7 + - - +
106P GLU* 4.9 4.4 - - - +
114P GLY* 3.5 2.1 - - - -
115P LYS* 2.9 42.3 + - + +
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Residues in contact with LEU 105 (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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16P PRO* 4.1 12.1 - - + +
19P LEU* 4.2 18.8 - - + -
20P PHE* 3.6 41.7 - - + +
23P LEU* 6.5 0.4 - - + -
24P VAL* 5.8 0.2 - - + -
79P ASN 3.6 0.3 - - - +
80P PHE* 3.0 27.8 + - + +
103P VAL* 4.1 18.2 - - + -
104P LYS* 1.3 104.2 + - - +
106P GLU* 1.3 62.2 + - - +
112P SER* 4.8 2.7 - - - +
113P LYS 3.4 6.7 - - - +
114P GLY* 3.9 14.8 - - - -
116P ILE* 4.5 10.1 - - + -
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Residues in contact with GLU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P PRO* 3.7 6.1 - - - -
80P PHE* 4.7 2.9 - - - -
104P LYS* 4.9 4.3 - - - +
105P LEU* 1.3 76.1 - - - +
107P ALA* 1.3 64.1 + - - +
108P VAL* 3.7 7.7 - - - +
112P SER* 3.4 2.9 - - - -
113P LYS* 3.0 63.6 + - + +
114P GLY* 5.8 0.2 - - - -
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Residues in contact with ALA 107 (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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16L PRO* 4.9 1.3 - - + -
78L ALA 4.6 2.8 - - - +
79L ASN* 5.4 5.0 + - - -
80L PHE* 4.0 21.3 - - + -
107L ALA* 3.8 26.0 - - + +
16P PRO* 3.3 25.5 - - + +
80P PHE* 5.1 1.4 - - - -
106P GLU* 1.3 72.8 - - - +
108P VAL* 1.3 75.1 + - - +
109P GLY 4.2 0.9 - - - +
111P GLY 3.5 0.9 - - - +
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Residues in contact with VAL 108 (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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78L ALA* 3.7 17.7 - - + +
79L ASN* 6.1 1.6 - - - +
205L 2AN 5.4 2.0 - - + -
106P GLU* 3.7 18.4 - - - +
107P ALA* 1.3 87.7 - - - +
109P GLY* 1.3 68.5 + - - +
110P GLY 3.1 0.5 + - - -
111P GLY* 2.7 29.3 + - - +
112P SER 4.8 0.4 - - - +
113P LYS* 3.9 44.9 - - + +
46R GLU* 5.2 9.4 - - - +
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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