Contacts of the strand formed by residues 97 - 110 (chain A) in PDB entry 4L8P
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 THR 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.9 0.5 - - - +
93A ASP* 3.0 31.5 + - - +
94A SER* 2.7 29.1 + - - +
96A ASN* 1.3 94.0 - - - +
98A ALA* 1.3 65.3 + - - +
130A TYR 3.4 10.8 - - - +
131A GLU* 4.9 4.5 - - + -
137A TRP* 3.7 5.5 - - - -
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Residues in contact with ALA 98 (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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23A ILE* 3.5 31.9 - - + -
91A THR 3.3 15.3 - - - +
92A ILE* 4.0 6.5 - - + -
93A ASP* 3.2 10.7 + - - +
97A THR* 1.3 79.6 - - - +
99A THR* 1.3 59.9 + - - +
129A LYS* 3.5 6.4 - - - +
130A TYR* 2.9 34.4 + - + +
137A TRP* 3.8 8.1 - - + -
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Residues in contact with THR 99 (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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89A GLU 3.8 1.0 - - - +
90A ILE* 3.4 4.5 - - - +
91A THR* 2.8 41.1 + - - +
93A ASP* 2.7 23.6 + - - -
98A ALA* 1.3 72.5 - - - +
100A GLY* 1.3 62.2 + - - +
101A ARG* 5.0 3.8 - - + +
127A THR* 3.6 28.3 - - + -
128A ASP 3.3 8.3 - - - +
129A LYS* 2.9 26.8 + - - +
130A TYR* 3.9 3.8 - - - -
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Residues in contact with GLY 100 (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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89A GLU 3.5 5.4 - - - -
90A ILE* 3.6 17.3 - - - -
99A THR* 1.3 75.6 - - - +
101A ARG* 1.3 64.9 + - - -
102A TRP* 3.6 6.1 - - - -
126A TYR 3.7 0.2 - - - +
127A THR* 3.5 1.5 - - - -
128A ASP* 2.7 43.1 + - - +
130A TYR* 3.5 10.0 - - - -
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Residues in contact with ARG 101 (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 THR 4.0 1.3 - - - +
88A PRO* 3.1 8.5 - - - +
89A GLU* 2.9 72.2 + - + +
99A THR* 5.3 2.9 - - + -
100A GLY* 1.3 74.0 - - - -
102A TRP* 1.3 63.8 + - - +
125A PHE* 5.8 6.5 - - - +
126A TYR 3.2 6.5 - - - +
127A THR* 3.7 32.4 + - + +
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Residues in contact with TRP 102 (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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23A ILE 4.6 0.4 - - - -
24A LYS* 4.0 27.4 - - + -
27A LYS* 3.5 36.9 - - + +
28A ALA* 5.3 0.7 - - - -
31A PHE* 4.8 2.2 - + - -
85A GLY* 4.4 13.9 - - - -
86A HIS* 4.0 21.1 - - - -
87A THR 4.7 0.7 - - - -
88A PRO* 3.6 41.7 - - + -
90A ILE* 3.8 12.1 - - + +
100A GLY 3.6 6.3 - - - -
101A ARG* 1.3 78.2 - - - +
103A TYR* 1.3 60.3 + - - +
104A LEU* 3.8 18.2 + - + -
125A PHE* 3.7 3.9 - - - +
126A TYR* 2.9 36.6 + - + +
128A ASP* 3.5 13.9 + - - -
130A TYR* 2.8 27.1 + - - -
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Residues in contact with TYR 103 (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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85A GLY 3.6 0.5 - - - -
86A HIS* 2.8 60.5 + + + +
87A THR* 3.5 18.1 + - - +
102A TRP* 1.3 70.2 - - - +
104A LEU* 1.3 70.8 + - - +
105A GLU* 6.0 1.6 - - + -
123A GLY* 5.4 1.3 - - - -
124A ALA 3.8 5.6 - - - -
125A PHE* 3.7 27.3 - + + -
147A ILE* 3.7 29.3 - - + +
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Residues in contact with LEU 104 (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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27A LYS* 5.3 0.9 - - - -
31A PHE* 3.6 40.8 - - + -
83A HIS* 4.1 11.2 - - + -
84A MSE 3.5 24.0 - - - +
85A GLY* 4.4 2.2 - - - -
102A TRP* 3.8 20.0 - - + -
103A TYR* 1.3 87.5 - - - +
105A GLU* 1.3 61.3 + - - +
106A ASP* 5.2 3.4 - - + +
123A GLY* 3.2 5.1 - - - -
124A ALA* 2.8 40.5 + - + +
126A TYR* 3.9 31.9 - - + -
204A 1PE 4.4 4.9 - - - +
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Residues in contact with GLU 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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82A MSE 3.6 1.9 - - - +
83A HIS* 3.6 0.9 - - - -
84A MSE 2.8 52.3 + - + +
86A HIS* 4.0 15.3 - - + -
103A TYR* 4.1 2.6 + - + -
104A LEU* 1.3 75.2 - - - +
106A ASP* 1.3 60.8 + - - +
107A ASN* 3.3 16.5 + - - +
121A ASN* 5.5 2.6 - - - +
122A GLY 3.5 13.5 - - - +
123A GLY* 4.4 0.4 - - - -
201A NI 4.2 10.0 - - - +
202A NA 2.6 28.2 - - - -
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Residues in contact with ASP 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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82A MSE 3.2 7.4 - - - +
83A HIS* 4.0 24.0 - - + +
104A LEU* 4.9 4.1 - - + +
105A GLU* 1.3 74.2 - - - +
107A ASN* 1.3 71.4 + - - +
108A LEU* 4.6 15.0 - - + +
120A ILE* 4.8 3.1 - - - +
121A ASN* 3.3 2.8 - - - -
122A GLY 3.0 35.5 + - - +
123A GLY* 4.1 1.2 - - - -
124A ALA 5.1 0.2 + - - -
146A ARG* 2.7 45.4 + - - -
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Residues in contact with ASN 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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80A ILE* 4.0 0.5 - - - +
81A SER* 3.4 1.6 - - - -
82A MSE 2.8 48.6 + - + +
84A MSE 3.7 19.3 - - - +
105A GLU* 3.3 18.8 + - - +
106A ASP* 1.3 90.0 - - - +
108A LEU* 1.3 64.2 + - - +
109A ILE* 5.4 7.0 - - + -
120A ILE 3.4 5.2 - - - -
121A ASN* 3.3 20.6 - - - +
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Residues in contact with LEU 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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75A MSE 4.8 0.9 - - + -
79A GLU* 3.5 29.6 - - + +
80A ILE 3.3 3.4 - - - +
81A SER* 3.6 18.6 - - - -
83A HIS* 4.1 17.3 - - + +
106A ASP* 4.6 10.8 - - + +
107A ASN* 1.3 85.1 - - - +
109A ILE* 1.3 66.4 + - - +
110A PHE* 4.4 7.0 - - + -
118A VAL 4.7 0.2 - - - -
119A GLY* 3.3 5.4 - - - -
120A ILE* 2.7 69.0 + - + +
121A ASN* 4.7 1.1 + - - +
152A PHE* 5.5 0.3 - - - -
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Residues in contact with ILE 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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78A GLU 3.6 0.9 - - - +
79A GLU* 3.4 1.8 - - - -
80A ILE* 2.8 60.5 + - + +
82A MSE 6.5 1.1 - - - -
107A ASN* 5.4 5.8 - - + -
108A LEU* 1.3 81.2 - - - +
110A PHE* 1.3 73.6 + - - +
111A THR* 3.9 12.7 + - + -
118A VAL 3.7 2.9 - - - -
119A GLY* 5.2 0.2 - - - -
154A ARG* 3.6 52.0 - - - +
160A ILE* 4.4 7.4 - - + -
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Residues in contact with PHE 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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74A ALA 5.4 0.7 - - - -
76A PRO* 5.1 7.4 - - + -
78A GLU* 3.3 13.2 - - + -
79A GLU* 3.3 46.9 - - + -
108A LEU* 4.7 6.1 - - + -
109A ILE* 1.3 79.2 - - - +
111A THR* 1.3 60.2 + - - +
112A ASP 3.6 3.6 - - - +
115A TYR* 3.1 50.5 - + + +
116A LYS* 4.5 0.2 - - - -
117A ASN* 2.8 29.2 + - - +
118A VAL* 3.0 29.5 + - + +
120A ILE* 4.1 24.9 - - + -
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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