Contacts of the strand formed by residues 87 - 99 (chain A) in PDB entry 5T4S
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A THR* 3.6 26.0 - - + -
81A LEU 3.4 12.3 - - - +
82A ARG* 3.7 19.3 - - + +
83A TYR 5.0 1.2 + - - -
86A GLY* 1.3 76.9 + - - -
88A VAL* 1.3 69.2 + - - +
89A SER* 5.7 0.9 - - - -
115A PRO* 3.1 33.8 - - - +
119A PHE* 3.6 3.4 - - - -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.8 34.1 - - + +
79A LEU 4.2 0.2 - - - +
80A THR* 3.4 3.6 - - - +
81A LEU* 2.8 56.7 + - + +
83A TYR* 4.0 4.5 - - + -
87A THR* 1.3 76.3 - - - +
89A SER* 1.3 60.7 + - - +
111A VAL* 3.8 31.0 - - + -
113A GLU 3.5 5.6 - - - +
114A MET* 4.1 5.4 - - + -
119A PHE* 3.5 29.4 - - + -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 5.0 4.0 + - - +
79A LEU 3.4 7.4 + - - -
80A THR* 3.3 21.7 + - - -
87A THR* 5.7 1.1 - - - -
88A VAL* 1.3 76.0 - - - +
90A GLY* 1.3 61.0 + - - +
111A VAL* 3.5 8.5 - - - +
112A THR* 2.9 21.4 + - - -
113A GLU* 2.9 42.3 + - - -
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 3.2 17.1 - - - +
79A LEU* 2.9 31.1 + - - +
89A SER* 1.3 77.6 + - - +
91A PHE* 1.3 62.9 + - - -
110A GLU 3.2 13.2 - - - -
111A VAL* 4.2 0.7 - - - -
112A THR* 3.4 14.8 - - - -
113A GLU* 5.4 0.2 - - - -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 4.2 0.7 - - - -
50A LYS* 3.8 29.6 - - + -
72A TYR* 4.8 7.2 - - - -
74A HIS* 5.7 2.5 - + - -
76A GLY* 3.7 22.7 - - - +
77A THR 3.1 13.0 - - - +
78A GLU* 4.2 9.0 - - - +
79A LEU* 3.6 7.1 - - - +
90A GLY* 1.3 77.2 - - - +
92A LEU* 1.3 69.2 + - - +
93A SER* 3.4 17.7 - - - -
109A GLY* 3.4 1.6 - - - -
110A GLU* 2.7 61.9 + - + +
112A THR* 3.7 26.5 - - + -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN* 5.1 0.7 - - - +
75A ASN* 3.7 12.7 + - - +
76A GLY 2.9 24.4 + - - -
77A THR* 2.8 35.7 + - + +
79A LEU* 3.7 31.9 - - + -
91A PHE* 1.3 77.5 - - - +
93A SER* 1.3 64.3 + - - +
107A MET* 3.8 26.0 - - + -
108A PHE* 3.4 23.6 - - - +
138A GLY* 5.2 12.3 - - - +
140A VAL* 4.5 22.2 - - + -
401A NAG 6.0 0.2 - - - -
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.4 19.5 + - - -
73A LYS 4.1 4.5 - - - -
75A ASN* 4.6 2.7 - - - +
91A PHE* 3.4 8.8 - - - -
92A LEU* 1.3 77.2 + - - +
94A GLN* 1.3 59.8 + - - +
107A MET* 3.2 7.3 - - - +
108A PHE* 2.8 48.5 + - - +
110A GLU* 2.7 35.9 + - - +
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Residues in contact with GLN 94 (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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71A SER 5.7 0.6 + - - -
72A TYR* 3.5 4.0 - - - -
73A LYS* 2.7 80.4 + - + +
74A HIS 5.7 0.2 - - - +
75A ASN* 6.0 0.2 - - + -
93A SER* 1.3 74.8 - - - +
95A ASP* 1.3 66.7 + - - +
105A THR* 3.3 32.2 - - + +
106A GLN 3.4 11.9 - - - +
107A MET* 4.1 22.4 - - + +
108A PHE* 4.0 0.9 - - - -
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Residues in contact with ASP 95 (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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26A ILE* 3.9 6.7 - - + -
27A GLY* 3.3 11.7 - - - -
64A PHE* 3.3 18.5 - - + -
69A SER* 2.6 23.7 + - - -
71A SER* 2.7 32.8 + - - -
72A TYR* 3.4 12.1 - - - -
94A GLN* 1.3 75.0 - - - +
96A ILE* 1.3 74.4 + - - +
97A ILE* 3.6 2.3 + - - +
105A THR* 4.4 5.2 - - - -
106A GLN* 2.9 34.2 + - - +
108A PHE* 3.6 19.4 - - + -
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Residues in contact with ILE 96 (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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25A GLY 3.7 0.7 - - - +
26A ILE* 3.4 4.2 - - - +
27A GLY 2.9 35.7 + - - +
28A THR* 4.3 7.0 - - - +
71A SER* 3.6 28.7 + - - +
95A ASP* 1.3 82.7 + - - +
97A ILE* 1.3 65.9 + - - +
98A THR* 5.0 5.8 - - + +
103A THR* 3.7 28.5 - - + +
104A VAL 3.6 4.0 - - - +
105A THR* 4.3 15.7 - - + +
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Residues in contact with ILE 97 (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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24A ILE* 4.1 17.5 - - + -
25A GLY 3.2 7.4 - - - +
26A ILE* 3.8 23.3 - - + -
44A VAL* 4.2 17.5 - - + -
95A ASP 4.1 3.4 - - - +
96A ILE* 1.3 79.8 - - - +
98A THR* 1.3 73.7 + - - +
99A VAL* 4.1 1.0 + - + -
102A ILE 3.5 1.7 - - - +
103A THR* 3.4 1.6 - - - -
104A VAL* 2.8 40.8 + - - +
106A GLN* 3.7 30.7 - - + -
108A PHE* 4.1 14.8 - - + -
143A ILE* 3.9 22.0 - - + -
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.3 12.3 - - - +
25A GLY* 2.8 49.2 + - - -
30A PRO* 4.9 9.5 - - + +
96A ILE* 5.0 4.9 - - + +
97A ILE* 1.3 73.4 - - - +
99A VAL* 1.3 61.1 + - - +
101A GLY* 5.2 8.5 - - - -
102A ILE 3.2 6.7 - - - +
103A THR* 3.1 29.2 - - + +
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Residues in contact with VAL 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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10A VAL* 3.7 21.1 - - + -
23A GLU 4.9 2.5 - - - -
24A ILE* 3.9 11.9 - - + -
37A PHE* 3.8 26.5 - - + -
97A ILE* 4.6 3.1 - - + +
98A THR* 1.3 77.9 - - - +
100A GLY* 1.3 61.5 + - - +
102A ILE* 2.9 31.0 + - - +
104A VAL* 4.8 1.8 - - + -
128A VAL* 6.1 0.2 - - + -
143A ILE* 4.0 26.5 - - + -
147A ILE* 4.2 17.7 - - + -
178A LEU* 4.1 13.5 - - + +
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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